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/7916156/working' mkdir: created directory `/scratch/stefan/7916156/working/protonate' Storing results in /scratch/stefan/7916156/finished Working in /scratch/stefan/7916156/working /scratch/stefan/7916156/working /scratch/stefan/7916156 /scratch/stefan/7916156/working/protonate /scratch/stefan/7916156/working /scratch/stefan/7916156 Precomputing protomers for all compounds (pH: 7.4) mv: cannot move `/nfs/home/stefan/.install4j_new' to `/nfs/home/stefan/.install4j': No such file or directory Jan 16, 2020 10:45:31 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. ph 7.4: 1036 protomers created Coalesing and merging protomers 1012 protomers generated for 1000 compounds Checking for new stereocenters and expanding 1014 protomers after new stereo-center expansion /scratch/stefan/7916156/working /scratch/stefan/7916156 Bulk generating 3D conformations all protomers in /scratch/stefan/7916156/working/3D mkdir: created directory `/scratch/stefan/7916156/working/3D' We are using corina for 3D embeding debuging info:: /scratch/stefan/7916156/working/protonate/xaaaabk-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' 1015 3D conformations generated for 1000 compounds Building REAL250005073893 mkdir: created directory `/scratch/stefan/7916156/working/building' mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073893' /scratch/stefan/7916156/working/building/REAL250005073893 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073893 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073893/0 /scratch/stefan/7916156/working/building/REAL250005073893 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 1) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/1 `/scratch/stefan/7916156/working/3D/1' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(=O)N1CC(F)(CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005073893.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073893/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073893 none CC(C)CC(=O)N1CC(F)(CNC(=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', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 15, 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, 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 167 conformations in input total number of sets (complete confs): 167 using faster count positions algorithm for large data unique positions, atoms: [167, 162, 167, 108, 75, 108, 75, 75, 31, 75, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 75, 167, 167, 167, 167, 167, 167, 167, 162, 162, 75, 75, 31, 31, 9, 1, 75, 75] 167 rigid atoms, others: [35, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37]) total number of confs: 650 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073893 none CC(C)CC(=O)N1CC(F)(CNC(=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', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 15, 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, 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 167 conformations in input total number of sets (complete confs): 167 using faster count positions algorithm for large data unique positions, atoms: [27, 26, 33, 7, 1, 7, 1, 1, 1, 1, 1, 10, 49, 49, 49, 75, 75, 75, 75, 75, 1, 33, 33, 33, 33, 33, 33, 33, 26, 26, 1, 1, 10, 10, 49, 75, 1, 1] 167 rigid atoms, others: [4, 37, 6, 7, 8, 9, 10, 20, 36, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35]) total number of confs: 336 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073893 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073893 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 mkdir: created directory `/scratch/stefan/7916156/finished' Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073893/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073893 Building REAL250005073894 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073894' /scratch/stefan/7916156/working/building/REAL250005073894 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073894 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073894/0 /scratch/stefan/7916156/working/building/REAL250005073894 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 2) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/2 `/scratch/stefan/7916156/working/3D/2' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC1C(=O)N1CC(F)(CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005073894.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073894/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073894 none CC1CC1C(=O)N1CC(F)(CNC(=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', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 15, 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, 7, 4, 7, 6, 7, 7, 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: [22, 22, 22, 6, 1, 6, 1, 1, 1, 1, 1, 10, 45, 45, 45, 60, 60, 60, 60, 60, 1, 22, 22, 22, 22, 22, 22, 22, 1, 1, 10, 10, 45, 60, 1, 1] 130 rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 10, 20, 28, 29] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33]) total number of confs: 197 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073894 none CC1CC1C(=O)N1CC(F)(CNC(=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', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 15, 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, 7, 4, 7, 6, 7, 7, 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, 8, 8, 22, 22, 22, 22, 62, 123, 123, 123, 130, 130, 130, 130, 130, 22, 1, 1, 1, 1, 1, 1, 1, 22, 22, 62, 62, 123, 130, 22, 22] 130 rigid atoms, others: [0, 1, 2, 3, 4, 21, 22, 23, 24, 25, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 388 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.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: REAL250005073894 none CC1CC1C(=O)N1CC(F)(CNC(=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', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 15, 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, 7, 4, 7, 6, 7, 7, 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, 85, 60, 85, 60, 60, 26, 60, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 60, 130, 130, 130, 130, 130, 130, 130, 60, 60, 25, 25, 9, 1, 60, 60] 130 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: 433 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073894 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073894 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073894/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073894 Building REAL250005073895 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073895' /scratch/stefan/7916156/working/building/REAL250005073895 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073895 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073895/0 /scratch/stefan/7916156/working/building/REAL250005073895 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 3) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/3 `/scratch/stefan/7916156/working/3D/3' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)=CC(=O)N1CC(F)(CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005073895.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073895.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073895/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073895 none CC(C)=CC(=O)N1CC(F)(CNC(=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', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 1, 11, 8, 5, 5, 15, 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, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 143 conformations in input total number of sets (complete confs): 143 using faster count positions algorithm for large data unique positions, atoms: [143, 143, 143, 106, 78, 106, 78, 78, 33, 78, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 78, 143, 143, 143, 143, 143, 143, 143, 78, 78, 32, 32, 9, 1, 78, 78] 143 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: 465 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073895 none CC(C)=CC(=O)N1CC(F)(CNC(=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', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 1, 11, 8, 5, 5, 15, 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, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 143 conformations in input total number of sets (complete confs): 143 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 7, 1, 7, 1, 1, 1, 1, 1, 9, 50, 50, 50, 78, 78, 78, 78, 78, 1, 27, 27, 27, 27, 27, 27, 27, 1, 1, 9, 9, 50, 78, 1, 1] 143 rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 10, 20, 28, 29] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33]) total number of confs: 237 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073895 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073895 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073895/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073895 Building REAL250005073896 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073896' /scratch/stefan/7916156/working/building/REAL250005073896 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073896 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073896/0 /scratch/stefan/7916156/working/building/REAL250005073896 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 4) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/4 `/scratch/stefan/7916156/working/3D/4' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC(=O)N1CC(F)(CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005073896.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073896/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073896 none CCCCC(=O)N1CC(F)(CNC(=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', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 15, 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, 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: [200, 196, 190, 76, 52, 76, 52, 52, 20, 52, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 52, 200, 201, 201, 201, 201, 196, 196, 190, 190, 52, 52, 19, 19, 4, 1, 52, 52] 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, 36, 37]) total number of confs: 798 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073896 none CCCCC(=O)N1CC(F)(CNC(=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', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 15, 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, 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: [51, 27, 18, 4, 1, 4, 1, 1, 1, 1, 1, 9, 39, 39, 39, 52, 52, 52, 52, 52, 1, 52, 54, 54, 51, 51, 33, 33, 18, 18, 1, 1, 9, 9, 39, 52, 1, 1] 201 rigid atoms, others: [4, 37, 6, 7, 8, 9, 10, 20, 36, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35]) total number of confs: 400 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073896 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073896 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073896/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073896 Building REAL250005073897 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073897' /scratch/stefan/7916156/working/building/REAL250005073897 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073897 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073897/0 /scratch/stefan/7916156/working/building/REAL250005073897 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 5) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/5 `/scratch/stefan/7916156/working/3D/5' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N1CC(F)(CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005073897.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073897/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073897 none CC(C)C(=O)N1CC(F)(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 1, 11, 8, 5, 5, 15, 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, 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 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [109, 102, 109, 71, 102, 71, 71, 35, 71, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 71, 109, 109, 109, 109, 109, 109, 109, 71, 71, 34, 34, 9, 1, 71, 71] 109 rigid atoms, others: [32, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34]) total number of confs: 366 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073897 none CC(C)C(=O)N1CC(F)(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 1, 11, 8, 5, 5, 15, 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, 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 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [20, 7, 20, 1, 7, 1, 1, 1, 1, 1, 10, 47, 47, 47, 71, 71, 71, 71, 71, 1, 20, 20, 20, 20, 20, 20, 20, 1, 1, 10, 10, 47, 71, 1, 1] 109 rigid atoms, others: [33, 34, 3, 5, 6, 7, 8, 9, 19, 27, 28] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32]) total number of confs: 228 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073897 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073897 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073897/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073897 Building REAL250005073898 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073898' /scratch/stefan/7916156/working/building/REAL250005073898 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073898 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073898/0 /scratch/stefan/7916156/working/building/REAL250005073898 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 6) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/6 `/scratch/stefan/7916156/working/3D/6' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)C(=O)N1CC(F)(CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005073898.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073898/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073898 none CCC(C)C(=O)N1CC(F)(CNC(=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', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 15, 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, 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 155 conformations in input total number of sets (complete confs): 155 using faster count positions algorithm for large data unique positions, atoms: [155, 154, 117, 154, 78, 117, 78, 78, 27, 78, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 78, 155, 155, 155, 155, 155, 154, 154, 154, 154, 78, 78, 27, 27, 7, 1, 78, 78] 155 rigid atoms, others: [35, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37]) total number of confs: 559 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073898 none CCC(C)C(=O)N1CC(F)(CNC(=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', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 15, 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, 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 155 conformations in input total number of sets (complete confs): 155 using faster count positions algorithm for large data unique positions, atoms: [25, 18, 6, 18, 1, 6, 1, 1, 1, 1, 1, 9, 50, 50, 50, 78, 78, 78, 78, 78, 1, 29, 29, 29, 29, 29, 18, 18, 18, 18, 1, 1, 9, 9, 50, 78, 1, 1] 155 rigid atoms, others: [4, 37, 6, 7, 8, 9, 10, 20, 36, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35]) total number of confs: 317 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073898 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073898 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073898/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073898 Building REAL250005073899 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073899' /scratch/stefan/7916156/working/building/REAL250005073899 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073899 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073899/0 /scratch/stefan/7916156/working/building/REAL250005073899 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 7) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/7 `/scratch/stefan/7916156/working/3D/7' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCC(=O)N1CC(F)(CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005073899.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073899/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073899 none C=CCCC(=O)N1CC(F)(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', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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: [1, 1, 5, 5, 1, 11, 8, 5, 5, 15, 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, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 180, 73, 44, 73, 44, 44, 13, 44, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 44, 201, 201, 201, 201, 201, 180, 180, 44, 44, 12, 12, 4, 1, 44, 44] 201 rigid atoms, others: [33, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35]) total number of confs: 819 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073899 none C=CCCC(=O)N1CC(F)(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', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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: [1, 1, 5, 5, 1, 11, 8, 5, 5, 15, 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, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [74, 35, 19, 5, 1, 5, 1, 1, 1, 1, 1, 7, 37, 37, 37, 44, 44, 44, 44, 44, 1, 74, 74, 74, 35, 35, 19, 19, 1, 1, 7, 7, 37, 44, 1, 1] 201 rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 10, 20, 28, 29] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33]) total number of confs: 383 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073899 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073899 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073899/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073899 Building REAL250005073900 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073900' /scratch/stefan/7916156/working/building/REAL250005073900 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073900 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073900/0 /scratch/stefan/7916156/working/building/REAL250005073900 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 8) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/8 `/scratch/stefan/7916156/working/3D/8' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C#N)C(=O)N1CC(F)(CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005073900.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073900/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073900 none CC(C#N)C(=O)N1CC(F)(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.1', 'N.1', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 11, 8, 5, 5, 15, 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, 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 134 conformations in input total number of sets (complete confs): 134 using faster count positions algorithm for large data unique positions, atoms: [134, 89, 134, 134, 63, 89, 63, 63, 28, 63, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 63, 134, 134, 134, 134, 63, 63, 27, 27, 8, 1, 63, 63] 134 rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32]) total number of confs: 522 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073900 none CC(C#N)C(=O)N1CC(F)(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.1', 'N.1', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 11, 8, 5, 5, 15, 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, 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 134 conformations in input total number of sets (complete confs): 134 using faster count positions algorithm for large data unique positions, atoms: [23, 7, 23, 23, 1, 7, 1, 1, 1, 1, 1, 9, 46, 46, 46, 63, 63, 63, 63, 63, 1, 23, 23, 23, 23, 1, 1, 9, 9, 46, 63, 1, 1] 134 rigid atoms, others: [32, 4, 6, 7, 8, 9, 10, 20, 25, 26, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 27, 28, 29, 30]) total number of confs: 221 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073900 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073900 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073900/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073900 Building REAL250005073901 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073901' /scratch/stefan/7916156/working/building/REAL250005073901 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073901 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073901/0 /scratch/stefan/7916156/working/building/REAL250005073901 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 9) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/9 `/scratch/stefan/7916156/working/3D/9' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=C(C)C(=O)N1CC(F)(CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005073901.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073901/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073901 none CC=C(C)C(=O)N1CC(F)(CNC(=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', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 1, 5, 1, 11, 8, 5, 5, 15, 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, 7, 4, 7, 6, 7, 7, 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, 108, 154, 60, 108, 60, 60, 22, 60, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 60, 154, 154, 154, 154, 154, 154, 154, 60, 60, 22, 22, 5, 1, 60, 60] 154 rigid atoms, others: [33, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35]) total number of confs: 513 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073901 none CC=C(C)C(=O)N1CC(F)(CNC(=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', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 1, 5, 1, 11, 8, 5, 5, 15, 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, 7, 4, 7, 6, 7, 7, 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: [30, 30, 7, 30, 1, 7, 1, 1, 1, 1, 1, 9, 43, 43, 43, 60, 60, 60, 60, 60, 1, 30, 30, 30, 30, 30, 30, 30, 1, 1, 9, 9, 43, 60, 1, 1] 154 rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 10, 20, 28, 29] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33]) total number of confs: 216 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073901 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073901 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073901/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073901 Building REAL250005073902 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073902' /scratch/stefan/7916156/working/building/REAL250005073902 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073902 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073902/0 /scratch/stefan/7916156/working/building/REAL250005073902 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 10) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/10 `/scratch/stefan/7916156/working/3D/10' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N1CC(F)(CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005073902.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073902/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073902 none CCC(=O)N1CC(F)(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 15, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 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 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [129, 98, 77, 98, 77, 77, 35, 77, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 77, 129, 129, 129, 129, 129, 77, 77, 35, 35, 10, 1, 77, 77] 129 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31]) total number of confs: 497 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073902 none CCC(=O)N1CC(F)(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 15, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 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 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [20, 7, 1, 7, 1, 1, 1, 1, 1, 10, 48, 48, 48, 77, 77, 77, 77, 77, 1, 20, 20, 20, 20, 20, 1, 1, 10, 10, 48, 77, 1, 1] 129 rigid atoms, others: [2, 4, 5, 6, 7, 8, 18, 24, 25, 30, 31] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 26, 27, 28, 29]) total number of confs: 237 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073902 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073902 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073902/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073902 Building REAL250005073903 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073903' /scratch/stefan/7916156/working/building/REAL250005073903 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073903 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073903/0 /scratch/stefan/7916156/working/building/REAL250005073903 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 11) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/11 `/scratch/stefan/7916156/working/3D/11' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC(F)(CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005073903.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073903/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073903 none CC(=O)N1CC(F)(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 15, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [45, 32, 45, 32, 32, 17, 32, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 32, 45, 45, 45, 32, 32, 16, 16, 9, 1, 32, 32] 45 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28]) total number of confs: 146 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073903 none CC(=O)N1CC(F)(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 15, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [3, 1, 3, 1, 1, 1, 1, 1, 10, 29, 29, 29, 32, 32, 32, 32, 32, 1, 4, 4, 4, 1, 1, 10, 10, 29, 32, 1, 1] 45 rigid atoms, others: [1, 3, 4, 5, 6, 7, 17, 21, 22, 27, 28] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 23, 24, 25, 26]) total number of confs: 96 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073903 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073903 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073903/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073903 Building REAL250005073904 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073904' /scratch/stefan/7916156/working/building/REAL250005073904 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073904 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073904/0 /scratch/stefan/7916156/working/building/REAL250005073904 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 12) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/12 `/scratch/stefan/7916156/working/3D/12' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(F)CN(C(=O)C2CC2)C1)C1=CC(=O)[N-]O1) `REAL250005073904.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073904/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073904 none O=C(NCC1(F)CN(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', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 15, 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] dock color type numbers: [6, 7, 4, 7, 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] 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: [130, 130, 68, 24, 24, 24, 24, 8, 1, 8, 1, 1, 1, 24, 130, 137, 137, 137, 137, 137, 130, 68, 68, 24, 24, 1, 1, 1, 1, 1, 24, 24, 137] 137 rigid atoms, others: [8, 10, 11, 12, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31, 32]) total number of confs: 424 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073904 none O=C(NCC1(F)CN(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', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 15, 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] dock color type numbers: [6, 7, 4, 7, 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] 0 hydrogens need rotated 137 conformations in input total number of sets (complete confs): 137 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 9, 1, 1, 1, 1, 1, 1, 7, 7, 24, 24, 1, 49, 79, 79, 79, 79, 79, 49, 9, 9, 1, 1, 24, 24, 24, 24, 24, 1, 1, 79] 137 rigid atoms, others: [3, 4, 5, 6, 7, 8, 13, 23, 24, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 32]) total number of confs: 231 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.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: REAL250005073904 none O=C(NCC1(F)CN(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', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 15, 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] dock color type numbers: [6, 7, 4, 7, 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] 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: [10, 1, 10, 10, 40, 79, 79, 79, 79, 105, 105, 137, 137, 79, 1, 1, 1, 1, 1, 1, 10, 39, 39, 79, 79, 137, 137, 137, 137, 137, 79, 79, 1] 137 rigid atoms, others: [32, 1, 14, 15, 16, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 459 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073904 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073904 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073904/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073904 Building REAL250005073905 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073905' /scratch/stefan/7916156/working/building/REAL250005073905 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073905 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073905/0 /scratch/stefan/7916156/working/building/REAL250005073905 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 13) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/13 `/scratch/stefan/7916156/working/3D/13' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(F)CN(C(=O)C2CCC2)C1)C1=CC(=O)[N-]O1) `REAL250005073905.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073905/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073905 none O=C(NCC1(F)CN(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', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 15, 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] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [148, 148, 86, 23, 23, 23, 23, 8, 1, 8, 1, 1, 1, 1, 23, 148, 156, 156, 156, 156, 156, 148, 86, 86, 23, 23, 1, 1, 1, 1, 1, 1, 1, 23, 23, 156] 156 rigid atoms, others: [32, 8, 10, 11, 12, 13, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 33, 34, 35]) total number of confs: 512 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073905 none O=C(NCC1(F)CN(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', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 15, 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] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 156 conformations in input total number of sets (complete confs): 156 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 9, 1, 1, 1, 1, 1, 1, 6, 6, 23, 23, 23, 1, 50, 90, 90, 90, 90, 90, 50, 9, 9, 1, 1, 23, 23, 23, 23, 23, 23, 23, 1, 1, 90] 156 rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 14, 24, 25] set([0, 1, 2, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 35]) total number of confs: 246 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.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: REAL250005073905 none O=C(NCC1(F)CN(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', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 15, 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] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [10, 1, 10, 10, 40, 91, 91, 91, 91, 134, 134, 156, 156, 156, 91, 1, 1, 1, 1, 1, 1, 11, 39, 39, 91, 91, 156, 156, 156, 156, 156, 156, 156, 91, 90, 1] 156 rigid atoms, others: [1, 35, 15, 16, 17, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 512 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073905 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073905 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073905/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073905 Building REAL250005073906 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073906' /scratch/stefan/7916156/working/building/REAL250005073906 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073906 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073906/0 /scratch/stefan/7916156/working/building/REAL250005073906 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 14) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/14 `/scratch/stefan/7916156/working/3D/14' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C(=O)N1CC(F)(CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005073906.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073906/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073906 none NC(=O)C(=O)N1CC(F)(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 11, 8, 5, 5, 15, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 77, 101, 56, 77, 56, 56, 21, 56, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 56, 101, 101, 56, 56, 21, 21, 6, 1, 56, 56] 101 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29]) total number of confs: 336 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073906 none NC(=O)C(=O)N1CC(F)(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 11, 8, 5, 5, 15, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 21, 1, 7, 1, 1, 1, 1, 1, 10, 44, 44, 44, 56, 56, 56, 56, 56, 1, 21, 21, 1, 1, 10, 10, 44, 56, 1, 1] 101 rigid atoms, others: [3, 5, 6, 7, 8, 9, 19, 22, 23, 28, 29] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 24, 25, 26, 27]) total number of confs: 182 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073906 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073906 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073906/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073906 Building REAL250005073907 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073907' /scratch/stefan/7916156/working/building/REAL250005073907 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073907 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073907/0 /scratch/stefan/7916156/working/building/REAL250005073907 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 15) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/15 `/scratch/stefan/7916156/working/3D/15' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C(=O)N1CC(F)(CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005073907.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073907/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073907 none CC(C)(C)C(=O)N1CC(F)(CNC(=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', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 15, 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, 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 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 67, 67, 53, 67, 53, 53, 23, 53, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 53, 67, 67, 67, 67, 67, 67, 67, 67, 67, 53, 53, 22, 22, 9, 1, 53, 53] 67 rigid atoms, others: [35, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37]) total number of confs: 215 number of broken/clashed sets: 65 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073907 none CC(C)(C)C(=O)N1CC(F)(CNC(=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', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 15, 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, 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 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [9, 7, 9, 9, 1, 7, 1, 1, 1, 1, 1, 9, 41, 41, 41, 53, 53, 53, 53, 53, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 9, 9, 41, 53, 1, 1] 67 rigid atoms, others: [4, 37, 6, 7, 8, 9, 10, 20, 36, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35]) total number of confs: 154 number of broken/clashed sets: 65 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073907 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073907 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073907/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073907 Building REAL250005073908 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073908' /scratch/stefan/7916156/working/building/REAL250005073908 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073908 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073908/0 /scratch/stefan/7916156/working/building/REAL250005073908 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 16) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/16 `/scratch/stefan/7916156/working/3D/16' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C(=O)N2CC(F)(CNC(=O)C3=CC(=O)[N-]O3)C2)CC1) `REAL250005073908.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073908.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073908/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073908 none CC1(C(=O)N2CC(F)(CNC(=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', 'F', 'C.3', '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'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 15, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [16, 7, 1, 7, 1, 1, 1, 1, 1, 10, 35, 35, 35, 42, 42, 42, 42, 42, 1, 16, 16, 16, 16, 16, 1, 1, 10, 10, 35, 42, 1, 1, 16, 16, 16, 16] 102 rigid atoms, others: [2, 4, 5, 6, 7, 8, 18, 24, 25, 30, 31] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 26, 27, 28, 29, 32, 33, 34, 35]) total number of confs: 150 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073908 none CC1(C(=O)N2CC(F)(CNC(=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', 'F', 'C.3', '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'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 15, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 5, 5, 16, 16, 16, 16, 49, 97, 97, 97, 102, 102, 102, 102, 102, 16, 1, 1, 2, 2, 2, 16, 16, 49, 49, 97, 102, 16, 16, 1, 1, 1, 1] 102 rigid atoms, others: [0, 1, 2, 35, 33, 32, 34, 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]) total number of confs: 307 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.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: REAL250005073908 none CC1(C(=O)N2CC(F)(CNC(=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', 'F', 'C.3', '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'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 15, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [102, 59, 42, 59, 42, 42, 18, 42, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 42, 102, 102, 102, 102, 102, 42, 42, 17, 17, 7, 1, 42, 42, 102, 102, 102, 102] 102 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, 34, 35]) total number of confs: 344 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073908 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073908 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073908/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073908 Building REAL250005073909 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073909' /scratch/stefan/7916156/working/building/REAL250005073909 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073909 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073909/0 /scratch/stefan/7916156/working/building/REAL250005073909 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 17) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/17 `/scratch/stefan/7916156/working/3D/17' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H]1C(=O)N1CC(F)(CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005073909.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073909/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073909 none C[C@@H]1C[C@H]1C(=O)N1CC(F)(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 15, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 33, 33, 6, 33, 1, 6, 1, 1, 1, 1, 1, 9, 51, 51, 51, 85, 85, 85, 85, 85, 1, 33, 33, 33, 33, 33, 1, 1, 9, 9, 51, 85, 1, 1] 178 rigid atoms, others: [34, 35, 6, 8, 9, 10, 11, 12, 22, 28, 29] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 30, 31, 32, 33]) total number of confs: 258 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073909 none C[C@@H]1C[C@H]1C(=O)N1CC(F)(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 15, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 9, 9, 33, 33, 33, 33, 102, 170, 170, 170, 178, 178, 178, 178, 178, 33, 2, 2, 2, 1, 1, 33, 33, 102, 102, 170, 178, 33, 33] 178 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 26, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35]) 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.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: REAL250005073909 none C[C@@H]1C[C@H]1C(=O)N1CC(F)(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 15, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [178, 178, 178, 178, 131, 178, 86, 131, 86, 86, 35, 86, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 86, 178, 178, 178, 178, 178, 86, 85, 34, 34, 8, 1, 86, 86] 178 rigid atoms, others: [33, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35]) total number of confs: 588 number of broken/clashed sets: 6 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073909 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073909 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073909/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073909 Building REAL250005073910 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073910' /scratch/stefan/7916156/working/building/REAL250005073910 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073910 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073910/0 /scratch/stefan/7916156/working/building/REAL250005073910 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 18) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/18 `/scratch/stefan/7916156/working/3D/18' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@@H]1C(=O)N1CC(F)(CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005073910.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073910/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073910 none C[C@H]1C[C@@H]1C(=O)N1CC(F)(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 15, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 32, 32, 7, 32, 1, 7, 1, 1, 1, 1, 1, 10, 53, 53, 53, 99, 99, 99, 99, 99, 1, 32, 32, 32, 32, 32, 1, 1, 10, 10, 53, 99, 1, 1] 187 rigid atoms, others: [34, 35, 6, 8, 9, 10, 11, 12, 22, 28, 29] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 30, 31, 32, 33]) total number of confs: 282 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073910 none C[C@H]1C[C@@H]1C(=O)N1CC(F)(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 15, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 8, 8, 32, 32, 32, 32, 98, 180, 180, 180, 187, 187, 187, 187, 187, 32, 2, 2, 2, 1, 1, 32, 32, 98, 98, 180, 187, 32, 32] 187 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 26, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 580 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.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: REAL250005073910 none C[C@H]1C[C@@H]1C(=O)N1CC(F)(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 15, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [187, 187, 187, 187, 145, 187, 99, 145, 99, 99, 42, 99, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 99, 187, 187, 187, 187, 187, 99, 99, 42, 42, 10, 1, 99, 99] 187 rigid atoms, others: [33, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35]) total number of confs: 611 number of broken/clashed sets: 7 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073910 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073910 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073910/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073910 Building REAL250005073911 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073911' /scratch/stefan/7916156/working/building/REAL250005073911 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073911 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073911/0 /scratch/stefan/7916156/working/building/REAL250005073911 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 19) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/19 `/scratch/stefan/7916156/working/3D/19' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CO)N1CC(F)(CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005073911.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073911/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073911 none O=C(CO)N1CC(F)(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 15, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 312 conformations in input total number of sets (complete confs): 312 using faster count positions algorithm for large data unique positions, atoms: [94, 70, 94, 104, 70, 70, 27, 70, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 70, 104, 104, 312, 70, 70, 26, 26, 8, 1, 70, 70] 312 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29]) total number of confs: 670 number of broken/clashed sets: 37 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073911 none O=C(CO)N1CC(F)(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 15, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 312 conformations in input total number of sets (complete confs): 312 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 26, 1, 1, 1, 1, 1, 10, 47, 47, 47, 70, 70, 70, 70, 70, 1, 26, 26, 78, 1, 1, 10, 10, 47, 70, 1, 1] 312 rigid atoms, others: [1, 4, 5, 6, 7, 8, 18, 22, 23, 28, 29] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 24, 25, 26, 27]) total number of confs: 320 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073911 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073911 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073911/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073911 Building REAL250005073912 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073912' /scratch/stefan/7916156/working/building/REAL250005073912 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073912 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073912/0 /scratch/stefan/7916156/working/building/REAL250005073912 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 20) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/20 `/scratch/stefan/7916156/working/3D/20' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(F)CN(C(=O)C2CCO2)C1)C1=CC(=O)[N-]O1) `REAL250005073912.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073912/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073912 none O=C(NCC1(F)CN(C(=O)C2CCO2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 15, 5, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 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: [152, 152, 85, 29, 29, 29, 29, 11, 1, 11, 1, 1, 1, 1, 29, 152, 158, 158, 158, 158, 158, 152, 85, 85, 29, 29, 1, 1, 1, 1, 1, 29, 29, 158] 158 rigid atoms, others: [8, 10, 11, 12, 13, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 31, 32, 33]) total number of confs: 499 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073912 none O=C(NCC1(F)CN(C(=O)C2CCO2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 15, 5, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 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: [49, 49, 10, 1, 1, 1, 1, 1, 1, 7, 7, 29, 29, 29, 1, 49, 76, 76, 76, 76, 76, 49, 10, 10, 1, 1, 29, 29, 29, 29, 29, 1, 1, 76] 158 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 14, 24, 25, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 33]) total number of confs: 237 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.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: REAL250005073912 none O=C(NCC1(F)CN(C(=O)C2CCO2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 15, 5, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 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: [8, 1, 8, 8, 27, 76, 76, 76, 76, 108, 108, 158, 158, 158, 76, 1, 1, 1, 1, 1, 1, 8, 27, 27, 76, 76, 158, 158, 158, 158, 158, 76, 76, 1] 158 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: 524 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073912 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073912 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073912/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073912 Building REAL250005073913 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073913' /scratch/stefan/7916156/working/building/REAL250005073913 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073913 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073913/0 /scratch/stefan/7916156/working/building/REAL250005073913 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 21) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/21 `/scratch/stefan/7916156/working/3D/21' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(F)CN(C(=O)C2COC2)C1)C1=CC(=O)[N-]O1) `REAL250005073913.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073913/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073913 none O=C(NCC1(F)CN(C(=O)C2COC2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 15, 5, 8, 1, 11, 5, 5, 12, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 138 conformations in input total number of sets (complete confs): 138 using faster count positions algorithm for large data unique positions, atoms: [128, 128, 70, 20, 20, 20, 20, 8, 1, 8, 1, 1, 1, 1, 20, 128, 138, 138, 138, 138, 138, 128, 70, 70, 20, 20, 1, 1, 1, 1, 1, 20, 20, 138] 138 rigid atoms, others: [8, 10, 11, 12, 13, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 31, 32, 33]) total number of confs: 440 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073913 none O=C(NCC1(F)CN(C(=O)C2COC2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 15, 5, 8, 1, 11, 5, 5, 12, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 138 conformations in input total number of sets (complete confs): 138 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 10, 1, 1, 1, 1, 1, 1, 6, 6, 20, 20, 20, 1, 50, 78, 78, 78, 78, 78, 50, 10, 10, 1, 1, 20, 20, 20, 20, 20, 1, 1, 78] 138 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 14, 24, 25, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 33]) total number of confs: 223 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.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: REAL250005073913 none O=C(NCC1(F)CN(C(=O)C2COC2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 15, 5, 8, 1, 11, 5, 5, 12, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 138 conformations in input total number of sets (complete confs): 138 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 32, 78, 78, 78, 78, 108, 108, 138, 138, 138, 78, 1, 1, 1, 1, 1, 1, 7, 31, 31, 78, 78, 138, 138, 138, 138, 138, 78, 78, 1] 138 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: 454 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073913 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073913 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073913/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073913 Building REAL250005073914 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073914' /scratch/stefan/7916156/working/building/REAL250005073914 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073914 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073914/0 /scratch/stefan/7916156/working/building/REAL250005073914 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 22) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/22 `/scratch/stefan/7916156/working/3D/22' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(C=CCO)N1CC(F)(CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005073914.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073914/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073914 none O=C(C=CCO)N1CC(F)(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 5, 12, 8, 5, 5, 15, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 65, 106, 189, 189, 201, 65, 65, 23, 65, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 65, 189, 189, 201, 201, 603, 65, 65, 23, 23, 5, 1, 65, 65] 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, 32, 33]) total number of confs: 1285 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073914 none O=C(C=CCO)N1CC(F)(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 5, 12, 8, 5, 5, 15, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 25, 25, 73, 1, 1, 1, 1, 1, 9, 44, 44, 44, 65, 65, 65, 65, 65, 1, 25, 24, 73, 73, 219, 1, 1, 9, 9, 44, 65, 1, 1] 603 rigid atoms, others: [32, 1, 33, 6, 7, 8, 9, 10, 20, 26, 27] set([0, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30, 31]) total number of confs: 617 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073914 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073914 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073914/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073914 Building REAL250005073915 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073915' /scratch/stefan/7916156/working/building/REAL250005073915 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073915 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073915/0 /scratch/stefan/7916156/working/building/REAL250005073915 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 23) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/23 `/scratch/stefan/7916156/working/3D/23' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC=CC(=O)N1CC(F)(CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005073915.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073915/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073915 none CCC=CC(=O)N1CC(F)(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 15, 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, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 165, 165, 101, 65, 101, 65, 65, 25, 65, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 65, 201, 201, 201, 201, 201, 165, 165, 65, 65, 25, 25, 6, 1, 65, 65] 201 rigid atoms, others: [33, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35]) total number of confs: 760 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073915 none CCC=CC(=O)N1CC(F)(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 15, 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, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 27, 6, 1, 6, 1, 1, 1, 1, 1, 9, 46, 46, 46, 65, 65, 65, 65, 65, 1, 47, 47, 47, 47, 47, 26, 27, 1, 1, 9, 9, 46, 65, 1, 1] 201 rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 10, 20, 28, 29] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33]) total number of confs: 318 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073915 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073915 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073915/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073915 Building REAL250005073916 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073916' /scratch/stefan/7916156/working/building/REAL250005073916 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073916 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073916/0 /scratch/stefan/7916156/working/building/REAL250005073916 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 24) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/24 `/scratch/stefan/7916156/working/3D/24' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCC(=O)N1CC(F)(CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005073916.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073916/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073916 none C#CCCC(=O)N1CC(F)(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 15, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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: [201, 201, 179, 86, 55, 86, 55, 55, 17, 55, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 55, 201, 201, 201, 179, 179, 55, 55, 17, 17, 5, 1, 55, 55] 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, 32, 33]) total number of confs: 793 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073916 none C#CCCC(=O)N1CC(F)(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 15, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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: [43, 43, 21, 6, 1, 6, 1, 1, 1, 1, 1, 9, 44, 44, 44, 55, 55, 55, 55, 55, 1, 43, 43, 43, 21, 21, 1, 1, 9, 9, 44, 55, 1, 1] 201 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 20, 26, 27] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30, 31]) total number of confs: 315 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073916 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073916 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073916/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073916 Building REAL250005073917 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073917' /scratch/stefan/7916156/working/building/REAL250005073917 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073917 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073917/0 /scratch/stefan/7916156/working/building/REAL250005073917 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 25) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/25 `/scratch/stefan/7916156/working/3D/25' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(O)C(=O)N1CC(F)(CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005073917.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073917/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073917 none C=CC(O)C(=O)N1CC(F)(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 11, 8, 5, 5, 15, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 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: [196, 196, 103, 196, 71, 103, 71, 71, 28, 71, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 71, 196, 196, 196, 196, 588, 71, 71, 28, 28, 7, 1, 71, 71] 588 rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33]) total number of confs: 1336 number of broken/clashed sets: 49 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073917 none C=CC(O)C(=O)N1CC(F)(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 11, 8, 5, 5, 15, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 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: [58, 27, 7, 27, 1, 7, 1, 1, 1, 1, 1, 10, 49, 49, 49, 71, 71, 71, 71, 71, 1, 58, 58, 58, 27, 81, 1, 1, 10, 10, 49, 71, 1, 1] 588 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 20, 26, 27] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30, 31]) total number of confs: 424 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073917 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073917 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073917/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073917 Building REAL250005073918 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073918' /scratch/stefan/7916156/working/building/REAL250005073918 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073918 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073918/0 /scratch/stefan/7916156/working/building/REAL250005073918 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 26) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/26 `/scratch/stefan/7916156/working/3D/26' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)C(=O)N1CC(F)(CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005073918.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073918/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073918 none CC(O)C(=O)N1CC(F)(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 15, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 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] 1 hydrogens need rotated 336 conformations in input total number of sets (complete confs): 336 using faster count positions algorithm for large data unique positions, atoms: [112, 67, 112, 53, 67, 53, 53, 20, 53, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 53, 112, 112, 112, 112, 336, 53, 53, 20, 20, 6, 1, 53, 53] 336 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32]) total number of confs: 771 number of broken/clashed sets: 63 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073918 none CC(O)C(=O)N1CC(F)(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 15, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 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] 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: [21, 7, 21, 1, 7, 1, 1, 1, 1, 1, 9, 43, 43, 43, 53, 53, 53, 53, 53, 1, 21, 21, 21, 21, 63, 1, 1, 9, 9, 43, 53, 1, 1] 336 rigid atoms, others: [32, 3, 5, 6, 7, 8, 9, 19, 25, 26, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 27, 28, 29, 30]) total number of confs: 253 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073918 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073918 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073918/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073918 Building REAL250005073919 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073919' /scratch/stefan/7916156/working/building/REAL250005073919 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073919 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073919/0 /scratch/stefan/7916156/working/building/REAL250005073919 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 27) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/27 `/scratch/stefan/7916156/working/3D/27' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)C(=O)N1CC(F)(CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005073919.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073919/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073919 none CC(=O)C(=O)N1CC(F)(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 11, 8, 5, 5, 15, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 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 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [129, 87, 129, 63, 87, 63, 63, 21, 63, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 63, 129, 129, 129, 63, 63, 21, 21, 7, 1, 63, 63] 129 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30]) total number of confs: 429 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073919 none CC(=O)C(=O)N1CC(F)(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 11, 8, 5, 5, 15, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 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 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [20, 7, 20, 1, 7, 1, 1, 1, 1, 1, 10, 48, 48, 48, 63, 63, 63, 63, 63, 1, 19, 20, 20, 1, 1, 10, 10, 48, 63, 1, 1] 129 rigid atoms, others: [3, 5, 6, 7, 8, 9, 19, 23, 24, 29, 30] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 25, 26, 27, 28]) total number of confs: 196 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073919 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073919 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073919/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073919 Building REAL250005073920 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073920' /scratch/stefan/7916156/working/building/REAL250005073920 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073920 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073920/0 /scratch/stefan/7916156/working/building/REAL250005073920 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 28) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/28 `/scratch/stefan/7916156/working/3D/28' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(F)CN(C(=O)C2(O)CC2)C1)C1=CC(=O)[N-]O1) `REAL250005073920.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073920/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073920 none O=C(NCC1(F)CN(C(=O)C2(O)CC2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 15, 5, 8, 1, 11, 5, 12, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 435 conformations in input total number of sets (complete confs): 435 using faster count positions algorithm for large data unique positions, atoms: [138, 138, 85, 27, 27, 27, 27, 8, 1, 8, 1, 1, 1, 1, 27, 138, 145, 145, 145, 145, 145, 138, 85, 85, 27, 27, 6, 1, 1, 1, 1, 27, 27, 145] 435 rigid atoms, others: [8, 10, 11, 12, 13, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33]) total number of confs: 455 number of broken/clashed sets: 53 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073920 none O=C(NCC1(F)CN(C(=O)C2(O)CC2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 15, 5, 8, 1, 11, 5, 12, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 435 conformations in input total number of sets (complete confs): 435 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 9, 1, 1, 1, 1, 1, 1, 7, 7, 27, 27, 27, 1, 50, 83, 83, 83, 83, 83, 50, 9, 9, 1, 1, 81, 27, 27, 27, 27, 1, 1, 83] 435 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 14, 24, 25, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 33]) total number of confs: 327 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.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: REAL250005073920 none O=C(NCC1(F)CN(C(=O)C2(O)CC2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 15, 5, 8, 1, 11, 5, 12, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 435 conformations in input total number of sets (complete confs): 435 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 33, 84, 84, 84, 84, 114, 114, 145, 145, 145, 84, 1, 1, 1, 1, 1, 1, 8, 32, 32, 84, 84, 435, 145, 145, 145, 145, 84, 83, 1] 435 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: 904 number of broken/clashed sets: 53 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073920 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073920 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073920/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073920 Building REAL250005073921 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073921' /scratch/stefan/7916156/working/building/REAL250005073921 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073921 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073921/0 /scratch/stefan/7916156/working/building/REAL250005073921 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 29) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/29 `/scratch/stefan/7916156/working/3D/29' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(F)CN(C(=O)C2=CCC2)C1)C1=CC(=O)[N-]O1) `REAL250005073921.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073921/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073921 none O=C(NCC1(F)CN(C(=O)C2=CCC2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 15, 5, 8, 1, 11, 1, 1, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [70, 70, 46, 18, 18, 18, 18, 10, 1, 10, 1, 1, 1, 1, 18, 70, 72, 72, 72, 72, 72, 70, 46, 46, 18, 18, 1, 1, 1, 1, 1, 18, 18, 72] 72 rigid atoms, others: [8, 10, 11, 12, 13, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 31, 32, 33]) total number of confs: 238 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073921 none O=C(NCC1(F)CN(C(=O)C2=CCC2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 15, 5, 8, 1, 11, 1, 1, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 9, 1, 1, 1, 1, 1, 1, 6, 6, 18, 17, 18, 1, 39, 53, 53, 53, 53, 53, 39, 9, 9, 1, 1, 18, 18, 18, 18, 18, 1, 1, 53] 72 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 14, 24, 25, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 33]) total number of confs: 163 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.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: REAL250005073921 none O=C(NCC1(F)CN(C(=O)C2=CCC2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 15, 5, 8, 1, 11, 1, 1, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [8, 1, 8, 8, 24, 53, 53, 53, 53, 72, 72, 72, 72, 72, 53, 1, 1, 1, 1, 1, 1, 8, 23, 23, 53, 53, 72, 72, 72, 72, 72, 53, 53, 1] 72 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: 224 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073921 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073921 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073921/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073921 Building REAL250005073922 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073922' /scratch/stefan/7916156/working/building/REAL250005073922 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073922 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073922/0 /scratch/stefan/7916156/working/building/REAL250005073922 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 30) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/30 `/scratch/stefan/7916156/working/3D/30' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC(=O)N1CC(F)(CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005073922.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073922/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073922 none CC=CC(=O)N1CC(F)(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 15, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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, 81, 63, 81, 63, 63, 28, 63, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 63, 100, 100, 100, 100, 100, 63, 63, 28, 28, 8, 1, 63, 63] 100 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32]) total number of confs: 334 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073922 none CC=CC(=O)N1CC(F)(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 15, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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: [25, 25, 7, 1, 7, 1, 1, 1, 1, 1, 9, 44, 44, 44, 63, 63, 63, 63, 63, 1, 25, 25, 25, 24, 25, 1, 1, 9, 9, 44, 63, 1, 1] 100 rigid atoms, others: [32, 3, 5, 6, 7, 8, 9, 19, 25, 26, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 27, 28, 29, 30]) total number of confs: 203 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073922 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073922 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073922/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073922 Building REAL250005073923 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073923' /scratch/stefan/7916156/working/building/REAL250005073923 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types Protomer extracton resulted in 0 protomers Marking REAL250005073923 as failed and skipping /scratch/stefan/7916156/working /scratch/stefan/7916156 mkdir: created directory `/scratch/stefan/7916156/failed' `/scratch/stefan/7916156/working/building/REAL250005073923' -> `/scratch/stefan/7916156/failed/REAL250005073923' Building REAL250005073924 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073924' /scratch/stefan/7916156/working/building/REAL250005073924 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073924 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073924/0 /scratch/stefan/7916156/working/building/REAL250005073924 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 31) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/31 `/scratch/stefan/7916156/working/3D/31' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)C(=O)N1CC(F)(CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005073924.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073924/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073924 none C[C@H](O)C(=O)N1CC(F)(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 15, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 354 conformations in input total number of sets (complete confs): 354 using faster count positions algorithm for large data unique positions, atoms: [118, 73, 118, 118, 59, 73, 59, 59, 23, 59, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 59, 118, 118, 118, 354, 59, 58, 23, 23, 6, 1, 59, 59] 354 rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32]) total number of confs: 812 number of broken/clashed sets: 66 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073924 none C[C@H](O)C(=O)N1CC(F)(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 15, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 354 conformations in input total number of sets (complete confs): 354 using faster count positions algorithm for large data unique positions, atoms: [21, 6, 21, 21, 1, 5, 1, 1, 1, 1, 1, 9, 42, 42, 42, 58, 58, 59, 58, 58, 1, 21, 21, 21, 63, 1, 1, 9, 9, 42, 58, 1, 1] 354 rigid atoms, others: [32, 4, 6, 7, 8, 9, 10, 20, 25, 26, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 27, 28, 29, 30]) total number of confs: 268 number of broken/clashed sets: 66 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073924 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073924 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073924/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073924 Building REAL250005073925 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073925' /scratch/stefan/7916156/working/building/REAL250005073925 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073925 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073925/0 /scratch/stefan/7916156/working/building/REAL250005073925 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 32) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/32 `/scratch/stefan/7916156/working/3D/32' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H]1C(=O)N1CC(F)(CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005073925.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073925/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073925 none C[C@@H]1C[C@H]1C(=O)N1CC(F)(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 15, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 33, 33, 6, 33, 1, 6, 1, 1, 1, 1, 1, 9, 51, 51, 51, 85, 85, 85, 85, 85, 1, 33, 33, 33, 33, 33, 1, 1, 9, 9, 51, 85, 1, 1] 178 rigid atoms, others: [34, 35, 6, 8, 9, 10, 11, 12, 22, 28, 29] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 30, 31, 32, 33]) total number of confs: 258 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073925 none C[C@@H]1C[C@H]1C(=O)N1CC(F)(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 15, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 9, 9, 33, 33, 33, 33, 102, 170, 170, 170, 178, 178, 178, 178, 178, 33, 2, 2, 2, 1, 1, 33, 33, 102, 102, 170, 178, 33, 33] 178 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 26, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35]) 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.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: REAL250005073925 none C[C@@H]1C[C@H]1C(=O)N1CC(F)(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 15, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [178, 178, 178, 178, 131, 178, 86, 131, 86, 86, 35, 86, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 86, 178, 178, 178, 178, 178, 86, 85, 34, 34, 8, 1, 86, 86] 178 rigid atoms, others: [33, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35]) total number of confs: 588 number of broken/clashed sets: 6 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073925 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073925 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073925/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073925 Building REAL250005073926 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073926' /scratch/stefan/7916156/working/building/REAL250005073926 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073926 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073926/0 /scratch/stefan/7916156/working/building/REAL250005073926 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 33) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/33 `/scratch/stefan/7916156/working/3D/33' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)CC(=O)N1CC(F)(CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005073926.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073926/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073926 none C=C(C)CC(=O)N1CC(F)(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', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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: [1, 1, 5, 5, 1, 11, 8, 5, 5, 15, 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, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 95, 61, 95, 61, 61, 21, 61, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 61, 201, 201, 201, 201, 201, 201, 201, 61, 61, 21, 21, 4, 1, 61, 61] 201 rigid atoms, others: [33, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35]) total number of confs: 769 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073926 none C=C(C)CC(=O)N1CC(F)(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', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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: [1, 1, 5, 5, 1, 11, 8, 5, 5, 15, 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, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 56, 7, 1, 7, 1, 1, 1, 1, 1, 9, 43, 43, 43, 61, 61, 61, 61, 61, 1, 56, 56, 56, 56, 56, 28, 28, 1, 1, 9, 9, 43, 61, 1, 1] 201 rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 10, 20, 28, 29] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 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 /scratch/stefan/7916156/working/building/REAL250005073926 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073926 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073926/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073926 Building REAL250005073927 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073927' /scratch/stefan/7916156/working/building/REAL250005073927 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073927 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073927/0 /scratch/stefan/7916156/working/building/REAL250005073927 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 34) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/34 `/scratch/stefan/7916156/working/3D/34' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(=O)N1CC(F)(CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005073927.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073927/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073927 none C=CCC(=O)N1CC(F)(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 15, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 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, 113, 75, 113, 75, 75, 33, 75, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 75, 201, 201, 201, 201, 201, 75, 75, 32, 32, 7, 1, 75, 75] 201 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32]) total number of confs: 801 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073927 none C=CCC(=O)N1CC(F)(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 15, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [65, 26, 5, 1, 5, 1, 1, 1, 1, 1, 9, 46, 46, 46, 75, 75, 75, 75, 75, 1, 65, 65, 65, 26, 26, 1, 1, 9, 9, 46, 75, 1, 1] 201 rigid atoms, others: [32, 3, 5, 6, 7, 8, 9, 19, 25, 26, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 27, 28, 29, 30]) total number of confs: 360 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073927 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073927 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073927/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073927 Building REAL250005073928 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073928' /scratch/stefan/7916156/working/building/REAL250005073928 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073928 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073928/0 /scratch/stefan/7916156/working/building/REAL250005073928 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 35) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/35 `/scratch/stefan/7916156/working/3D/35' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCC(=O)N1CC(F)(CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005073928.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073928/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073928 none N#CCC(=O)N1CC(F)(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 1, 11, 8, 5, 5, 15, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 176 conformations in input total number of sets (complete confs): 176 using faster count positions algorithm for large data unique positions, atoms: [176, 176, 112, 80, 112, 80, 80, 32, 80, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 80, 176, 176, 80, 80, 31, 31, 11, 1, 80, 80] 176 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29]) total number of confs: 684 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073928 none N#CCC(=O)N1CC(F)(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 1, 11, 8, 5, 5, 15, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 176 conformations in input total number of sets (complete confs): 176 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 6, 1, 6, 1, 1, 1, 1, 1, 10, 50, 50, 50, 80, 80, 80, 80, 80, 1, 30, 30, 1, 1, 10, 10, 50, 80, 1, 1] 176 rigid atoms, others: [3, 5, 6, 7, 8, 9, 19, 22, 23, 28, 29] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 24, 25, 26, 27]) total number of confs: 266 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073928 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073928 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073928/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073928 Building REAL250005073929 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073929' /scratch/stefan/7916156/working/building/REAL250005073929 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073929 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073929/0 /scratch/stefan/7916156/working/building/REAL250005073929 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 36) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/36 `/scratch/stefan/7916156/working/3D/36' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCF)N1CC(F)(CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005073929.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073929/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073929 none O=C(CCF)N1CC(F)(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'C.3', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 15, 8, 5, 5, 15, 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: [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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [103, 70, 103, 201, 201, 70, 70, 29, 70, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 70, 201, 201, 201, 201, 70, 70, 28, 28, 7, 1, 70, 70] 201 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31]) total number of confs: 772 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073929 none O=C(CCF)N1CC(F)(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'C.3', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 15, 8, 5, 5, 15, 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: [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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 21, 44, 1, 1, 1, 1, 1, 9, 47, 47, 47, 70, 70, 70, 70, 70, 1, 21, 21, 44, 44, 1, 1, 9, 9, 47, 70, 1, 1] 201 rigid atoms, others: [1, 5, 6, 7, 8, 9, 19, 24, 25, 30, 31] set([0, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 26, 27, 28, 29]) total number of confs: 333 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073929 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073929 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073929/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073929 Building REAL250005073930 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073930' /scratch/stefan/7916156/working/building/REAL250005073930 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073930 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073930/0 /scratch/stefan/7916156/working/building/REAL250005073930 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 37) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/37 `/scratch/stefan/7916156/working/3D/37' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)C(=O)N1CC(F)(CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005073930.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073930/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073930 none C[C@@H](O)C(=O)N1CC(F)(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 15, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 336 conformations in input total number of sets (complete confs): 336 using faster count positions algorithm for large data unique positions, atoms: [112, 67, 112, 112, 53, 67, 53, 52, 21, 53, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 53, 112, 112, 112, 336, 53, 52, 21, 21, 6, 1, 53, 53] 336 rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32]) total number of confs: 775 number of broken/clashed sets: 63 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073930 none C[C@@H](O)C(=O)N1CC(F)(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 15, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [20, 5, 20, 20, 1, 5, 1, 1, 1, 1, 1, 8, 41, 41, 41, 52, 52, 52, 52, 52, 1, 20, 20, 20, 60, 1, 1, 8, 8, 41, 52, 1, 1] 336 rigid atoms, others: [32, 4, 6, 7, 8, 9, 10, 20, 25, 26, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 27, 28, 29, 30]) total number of confs: 245 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073930 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073930 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073930/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073930 Building REAL250005073931 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073931' /scratch/stefan/7916156/working/building/REAL250005073931 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073931 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073931/0 /scratch/stefan/7916156/working/building/REAL250005073931 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 38) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/38 `/scratch/stefan/7916156/working/3D/38' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C1CC1C(=O)N1CC(F)(CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005073931.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073931/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073931 none C=C1CC1C(=O)N1CC(F)(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', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 15, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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 185 conformations in input total number of sets (complete confs): 185 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 36, 7, 1, 7, 1, 1, 1, 1, 1, 10, 50, 50, 50, 77, 77, 77, 77, 77, 1, 36, 36, 36, 36, 36, 1, 1, 10, 10, 50, 77, 1, 1] 185 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 20, 26, 27] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30, 31]) total number of confs: 254 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073931 none C=C1CC1C(=O)N1CC(F)(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', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 15, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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 185 conformations in input total number of sets (complete confs): 185 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 12, 12, 36, 36, 36, 36, 102, 178, 178, 178, 185, 185, 185, 185, 185, 36, 1, 1, 1, 1, 1, 36, 36, 102, 102, 178, 185, 36, 36] 185 rigid atoms, others: [0, 1, 2, 3, 4, 21, 22, 23, 24, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 578 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.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: REAL250005073931 none C=C1CC1C(=O)N1CC(F)(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', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 15, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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 185 conformations in input total number of sets (complete confs): 185 using faster count positions algorithm for large data unique positions, atoms: [185, 185, 185, 119, 77, 119, 77, 77, 34, 77, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 77, 185, 185, 185, 185, 185, 77, 77, 34, 34, 9, 1, 77, 77] 185 rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33]) total number of confs: 594 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073931 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073931 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073931/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073931 Building REAL250005073932 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073932' /scratch/stefan/7916156/working/building/REAL250005073932 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073932 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073932/0 /scratch/stefan/7916156/working/building/REAL250005073932 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 39) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/39 `/scratch/stefan/7916156/working/3D/39' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC1C(=O)N1CC(F)(CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005073932.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073932/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073932 none CC1=CC1C(=O)N1CC(F)(CNC(=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', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 15, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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: [38, 38, 38, 6, 1, 6, 1, 1, 1, 1, 1, 8, 47, 47, 47, 77, 77, 77, 77, 77, 1, 38, 38, 38, 38, 38, 1, 1, 8, 8, 47, 78, 1, 1] 201 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 20, 26, 27] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30, 31]) total number of confs: 257 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073932 none CC1=CC1C(=O)N1CC(F)(CNC(=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', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 15, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 11, 11, 38, 38, 38, 38, 104, 193, 193, 193, 201, 201, 201, 201, 201, 38, 2, 2, 2, 1, 1, 38, 38, 104, 104, 193, 201, 38, 38] 201 rigid atoms, others: [0, 1, 2, 3, 4, 24, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33]) 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.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: REAL250005073932 none CC1=CC1C(=O)N1CC(F)(CNC(=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', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 15, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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: [201, 201, 201, 114, 78, 114, 78, 78, 34, 78, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 78, 201, 201, 201, 201, 201, 78, 77, 33, 33, 10, 1, 78, 78] 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, 32, 33]) total number of confs: 637 number of broken/clashed sets: 6 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073932 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073932 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073932/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073932 Building REAL250005073933 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073933' /scratch/stefan/7916156/working/building/REAL250005073933 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073933 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073933/0 /scratch/stefan/7916156/working/building/REAL250005073933 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 40) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/40 `/scratch/stefan/7916156/working/3D/40' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(=O)N1CC(F)(CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005073933.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073933/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073933 none C=CC(=O)N1CC(F)(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 15, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [75, 75, 49, 75, 49, 49, 19, 49, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 49, 75, 75, 75, 49, 49, 19, 19, 7, 1, 49, 49] 75 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29]) total number of confs: 236 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073933 none C=CC(=O)N1CC(F)(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 15, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [14, 6, 1, 6, 1, 1, 1, 1, 1, 9, 39, 39, 39, 49, 49, 49, 49, 49, 1, 14, 14, 14, 1, 1, 9, 9, 39, 49, 1, 1] 75 rigid atoms, others: [2, 4, 5, 6, 7, 8, 18, 22, 23, 28, 29] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 24, 25, 26, 27]) total number of confs: 153 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073933 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073933 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073933/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073933 Building REAL250005073934 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073934' /scratch/stefan/7916156/working/building/REAL250005073934 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073934 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073934/0 /scratch/stefan/7916156/working/building/REAL250005073934 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 41) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/41 `/scratch/stefan/7916156/working/3D/41' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NC[C@@H]1CC(C)(C)CN1C(=O)C1=CC(=O)[N-]O1) `REAL250005073934.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073934/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073934 none CCC(=O)NC[C@@H]1CC(C)(C)CN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [111, 94, 94, 94, 64, 24, 24, 24, 24, 24, 24, 24, 24, 10, 1, 10, 1, 1, 1, 1, 1, 1, 111, 111, 111, 111, 111, 94, 64, 64, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1] 111 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: 423 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073934 none CCC(=O)NC[C@@H]1CC(C)(C)CN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [78, 27, 27, 27, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 24, 24, 24, 24, 24, 78, 78, 78, 78, 78, 27, 9, 9, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 24] 111 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 39, 38, 30, 31] set([0, 1, 2, 3, 4, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 40]) total number of confs: 335 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073934 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073934 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073934/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073934 Building REAL250005073935 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073935' /scratch/stefan/7916156/working/building/REAL250005073935 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073935 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073935/0 /scratch/stefan/7916156/working/building/REAL250005073935 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 42) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/42 `/scratch/stefan/7916156/working/3D/42' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC[C@@H]1CC(C)(C)CN1C(=O)C1=CC(=O)[N-]O1) `REAL250005073935.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073935/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073935 none CC(=O)NC[C@@H]1CC(C)(C)CN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.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, 7, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 45, 43, 21, 21, 21, 21, 21, 21, 21, 21, 9, 1, 9, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 43, 43, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1] 45 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: 138 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073935 none CC(=O)NC[C@@H]1CC(C)(C)CN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.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, 7, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 21, 21, 21, 21, 21, 25, 25, 25, 25, 9, 9, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 21] 45 rigid atoms, others: [35, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 36, 27, 28] set([0, 1, 2, 3, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 37]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073935 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073935 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073935/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073935 Building REAL250005073936 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073936' /scratch/stefan/7916156/working/building/REAL250005073936 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073936 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073936/0 /scratch/stefan/7916156/working/building/REAL250005073936 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 43) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/43 `/scratch/stefan/7916156/working/3D/43' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)C[C@@H](CNC(=O)CO)N(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005073936.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073936/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073936 none CC1(C)C[C@@H](CNC(=O)CO)N(C(=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.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', '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, 5, 8, 1, 11, 5, 12, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 12, 12, 12, 12, 20, 31, 31, 31, 36, 5, 1, 5, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 20, 20, 31, 36, 36, 108, 1, 12, 12] 108 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: 234 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073936 none CC1(C)C[C@@H](CNC(=O)CO)N(C(=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.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', '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, 5, 8, 1, 11, 5, 12, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 16, 16, 16, 35, 1, 1, 5, 5, 12, 12, 12, 12, 12, 1, 2, 2, 2, 2, 2, 2, 1, 1, 6, 6, 16, 35, 35, 105, 12, 1, 1] 108 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 12, 13, 21, 38, 28, 29, 37] set([7, 8, 9, 10, 11, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 266 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073936 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073936 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073936/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073936 Building REAL250005073937 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073937' /scratch/stefan/7916156/working/building/REAL250005073937 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073937 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073937/0 /scratch/stefan/7916156/working/building/REAL250005073937 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 44) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/44 `/scratch/stefan/7916156/working/3D/44' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N1CC(C)(C)C[C@H]1CNC(=O)C1=CC(=O)[N-]O1) `REAL250005073937.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073937.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073937/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073937 none CCC(=O)N1CC(C)(C)C[C@H]1CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [36, 32, 27, 32, 27, 27, 27, 27, 27, 27, 16, 27, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 36, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 16, 16, 8, 1] 36 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: 125 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073937 none CCC(=O)N1CC(C)(C)C[C@H]1CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 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, 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: [8, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 20, 20, 20, 27, 27, 27, 27, 27, 8, 8, 8, 8, 8, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 7, 7, 20, 27] 36 rigid atoms, others: [2, 35, 4, 5, 6, 7, 8, 9, 10, 11, 12, 36, 27, 28] set([0, 1, 3, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073937 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073937 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073937/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073937 Building REAL250005073938 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073938' /scratch/stefan/7916156/working/building/REAL250005073938 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073938 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073938/0 /scratch/stefan/7916156/working/building/REAL250005073938 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 45) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/45 `/scratch/stefan/7916156/working/3D/45' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC(C)(C)C[C@H]1CNC(=O)C1=CC(=O)[N-]O1) `REAL250005073938.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073938.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073938/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073938 none CC(=O)N1CC(C)(C)C[C@H]1CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [31, 30, 31, 30, 30, 30, 30, 30, 30, 18, 30, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 31, 31, 31, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 18, 18, 7, 1] 31 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: 105 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073938 none CC(=O)N1CC(C)(C)C[C@H]1CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 24, 24, 24, 30, 30, 30, 30, 30, 5, 5, 5, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 8, 8, 24, 30] 31 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 33] set([0, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37]) total number of confs: 104 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073938 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073938 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073938/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073938 Building REAL250005073939 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073939' /scratch/stefan/7916156/working/building/REAL250005073939 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073939 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073939/0 /scratch/stefan/7916156/working/building/REAL250005073939 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 46) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/46 `/scratch/stefan/7916156/working/3D/46' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)N(C(=O)CO)C1) `REAL250005073939.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073939/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073939 none CC1(C)C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)N(C(=O)CO)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 24, 24, 15, 24, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 24, 24, 30, 30, 34, 24, 24, 24, 24, 24, 24, 24, 24, 24, 15, 15, 8, 1, 34, 34, 102, 24, 24] 102 rigid atoms, others: [33, 8, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38]) total number of confs: 217 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073939 none CC1(C)C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)N(C(=O)CO)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 8, 20, 20, 20, 24, 24, 24, 24, 24, 1, 1, 5, 5, 11, 1, 2, 2, 2, 2, 2, 2, 1, 1, 8, 8, 20, 24, 11, 11, 33, 1, 1] 102 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 16, 17, 21, 38, 28, 29, 37] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 149 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073939 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073939 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073939/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073939 Building REAL250005073940 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073940' /scratch/stefan/7916156/working/building/REAL250005073940 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073940 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073940/0 /scratch/stefan/7916156/working/building/REAL250005073940 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 47) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/47 `/scratch/stefan/7916156/working/3D/47' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(=O)N1CC(C)(C)C[C@H]1CNC(=O)C1=CC(=O)[N-]O1) `REAL250005073940.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073940/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073940 none C=CC(=O)N1CC(C)(C)C[C@H]1CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 26, 31, 26, 26, 26, 26, 26, 26, 17, 26, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 31, 31, 31, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 17, 17, 7, 1] 31 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: 104 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073940 none C=CC(=O)N1CC(C)(C)C[C@H]1CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 19, 19, 19, 26, 26, 26, 26, 26, 15, 15, 15, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 7, 7, 19, 26] 31 rigid atoms, others: [33, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 34, 25, 26] set([0, 1, 3, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073940 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073940 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073940/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073940 Building REAL250005073941 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073941' /scratch/stefan/7916156/working/building/REAL250005073941 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073941 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073941/0 /scratch/stefan/7916156/working/building/REAL250005073941 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 48) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/48 `/scratch/stefan/7916156/working/3D/48' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NCC1CC(C)(C)CN1C(=O)C1=CC(=O)[N-]O1) `REAL250005073941.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073941.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073941/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073941 none CCC(=O)NCC1CC(C)(C)CN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 110 conformations in input total number of sets (complete confs): 110 using faster count positions algorithm for large data unique positions, atoms: [110, 94, 94, 94, 67, 25, 25, 25, 25, 25, 25, 25, 10, 1, 10, 1, 1, 1, 1, 1, 1, 110, 110, 110, 110, 110, 94, 67, 67, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1] 110 rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 414 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073941 none CCC(=O)NCC1CC(C)(C)CN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 110 conformations in input total number of sets (complete confs): 110 using faster count positions algorithm for large data unique positions, atoms: [75, 24, 24, 24, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 25, 25, 25, 25, 25, 75, 75, 75, 75, 75, 24, 8, 8, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 25] 110 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 39, 38, 29, 30, 31] set([0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 40]) total number of confs: 326 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073941 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073941 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073941/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073941 Building REAL250005073942 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073942' /scratch/stefan/7916156/working/building/REAL250005073942 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073942 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073942/0 /scratch/stefan/7916156/working/building/REAL250005073942 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 49) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/49 `/scratch/stefan/7916156/working/3D/49' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC1CC(C)(C)CN1C(=O)C1=CC(=O)[N-]O1) `REAL250005073942.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073942.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073942/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073942 none CC(=O)NCC1CC(C)(C)CN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 45, 43, 19, 19, 19, 19, 19, 19, 19, 8, 1, 8, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 43, 43, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1] 45 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: 152 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073942 none CC(=O)NCC1CC(C)(C)CN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 19, 19, 19, 19, 19, 25, 25, 25, 25, 9, 9, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 19] 45 rigid atoms, others: [35, 4, 5, 6, 7, 8, 9, 10, 11, 12, 36, 26, 27, 28] set([0, 1, 2, 3, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 37]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073942 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073942 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073942/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073942 Building REAL250005073943 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073943' /scratch/stefan/7916156/working/building/REAL250005073943 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073943 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073943/0 /scratch/stefan/7916156/working/building/REAL250005073943 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 50) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/50 `/scratch/stefan/7916156/working/3D/50' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CC(CNC(=O)CO)N(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005073943.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073943/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073943 none CC1(C)CC(CNC(=O)CO)N(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 12, 12, 12, 20, 31, 31, 31, 37, 5, 1, 5, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 20, 20, 31, 37, 37, 111, 1, 12, 12] 111 rigid atoms, others: [36, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 243 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073943 none CC1(C)CC(CNC(=O)CO)N(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 16, 16, 16, 36, 1, 1, 5, 5, 12, 12, 12, 12, 12, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1, 6, 6, 16, 36, 36, 108, 12, 1, 1] 111 rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 11, 12, 20, 27, 28, 29, 37] set([6, 7, 8, 9, 10, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 275 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073943 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073943 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073943/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073943 Building REAL250005073944 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073944' /scratch/stefan/7916156/working/building/REAL250005073944 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073944 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073944/0 /scratch/stefan/7916156/working/building/REAL250005073944 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 51) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/51 `/scratch/stefan/7916156/working/3D/51' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N1CC(C)(C)CC1CNC(=O)C1=CC(=O)[N-]O1) `REAL250005073944.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073944/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073944 none CCC(=O)N1CC(C)(C)CC1CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [35, 31, 27, 31, 27, 27, 27, 27, 27, 27, 16, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 35, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 16, 16, 7, 1] 35 rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 122 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073944 none CCC(=O)N1CC(C)(C)CC1CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 7, 20, 20, 20, 27, 27, 27, 27, 27, 7, 7, 7, 7, 7, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1, 7, 7, 20, 27] 35 rigid atoms, others: [2, 35, 4, 5, 6, 7, 8, 9, 10, 11, 34, 36, 26, 27] set([0, 1, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073944 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073944 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073944/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073944 Building REAL250005073945 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073945' /scratch/stefan/7916156/working/building/REAL250005073945 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073945 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073945/0 /scratch/stefan/7916156/working/building/REAL250005073945 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 52) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/52 `/scratch/stefan/7916156/working/3D/52' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC(C)(C)CC1CNC(=O)C1=CC(=O)[N-]O1) `REAL250005073945.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073945/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073945 none CC(=O)N1CC(C)(C)CC1CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [31, 30, 31, 30, 30, 30, 30, 30, 30, 18, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 31, 31, 31, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 18, 18, 6, 1] 31 rigid atoms, others: [37, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 103 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073945 none CC(=O)N1CC(C)(C)CC1CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 24, 24, 24, 30, 30, 30, 30, 30, 5, 5, 5, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1, 8, 8, 24, 30] 31 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 33, 31] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37]) total number of confs: 104 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073945 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073945 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073945/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073945 Building REAL250005073946 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073946' /scratch/stefan/7916156/working/building/REAL250005073946 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073946 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073946/0 /scratch/stefan/7916156/working/building/REAL250005073946 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 53) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/53 `/scratch/stefan/7916156/working/3D/53' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CC(CNC(=O)C2=CC(=O)[N-]O2)N(C(=O)CO)C1) `REAL250005073946.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073946.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073946/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073946 none CC1(C)CC(CNC(=O)C2=CC(=O)[N-]O2)N(C(=O)CO)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 23, 23, 15, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 23, 23, 28, 28, 32, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 15, 15, 7, 1, 32, 32, 96, 23, 23] 96 rigid atoms, others: [33, 7, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38]) total number of confs: 206 number of broken/clashed sets: 11 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073946 none CC1(C)CC(CNC(=O)C2=CC(=O)[N-]O2)N(C(=O)CO)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 7, 18, 18, 18, 23, 23, 23, 23, 23, 1, 1, 5, 5, 12, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1, 7, 7, 18, 23, 12, 12, 36, 1, 1] 96 rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 15, 16, 20, 27, 28, 29, 37] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 17, 18, 19, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 150 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073946 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073946 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073946/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073946 Building REAL250005073947 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073947' /scratch/stefan/7916156/working/building/REAL250005073947 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073947 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073947/0 /scratch/stefan/7916156/working/building/REAL250005073947 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 54) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/54 `/scratch/stefan/7916156/working/3D/54' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(=O)N1CC(C)(C)CC1CNC(=O)C1=CC(=O)[N-]O1) `REAL250005073947.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073947/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073947 none C=CC(=O)N1CC(C)(C)CC1CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 26, 31, 26, 26, 26, 26, 26, 26, 16, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 31, 31, 31, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 16, 16, 7, 1] 31 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: 102 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073947 none C=CC(=O)N1CC(C)(C)CC1CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 18, 18, 18, 26, 26, 26, 26, 26, 15, 15, 15, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1, 7, 7, 18, 26] 31 rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 9, 10, 11, 34, 24, 25] set([0, 1, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073947 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073947 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073947/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073947 Building REAL250005073948 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073948' /scratch/stefan/7916156/working/building/REAL250005073948 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073948 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073948/0 /scratch/stefan/7916156/working/building/REAL250005073948 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 55) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/55 `/scratch/stefan/7916156/working/3D/55' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NCC12CC1CN(C(=O)C1=CC(=O)[N-]O1)C2) `REAL250005073948.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073948/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073948 none CCC(=O)NCC12CC1CN(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 157, 157, 157, 78, 23, 23, 23, 23, 23, 9, 1, 9, 1, 1, 1, 1, 1, 1, 23, 201, 201, 201, 201, 201, 157, 78, 78, 23, 23, 23, 23, 23, 1, 23, 23] 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: 753 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073948 none CCC(=O)NCC12CC1CN(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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: [152, 52, 52, 52, 10, 1, 1, 1, 1, 1, 1, 1, 6, 6, 23, 23, 23, 23, 23, 1, 152, 152, 152, 152, 152, 52, 10, 10, 1, 1, 1, 1, 1, 23, 1, 1] 201 rigid atoms, others: [32, 34, 35, 5, 6, 7, 8, 9, 10, 11, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 33, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 590 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073948 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073948 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073948/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073948 Building REAL250005073949 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073949' /scratch/stefan/7916156/working/building/REAL250005073949 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073949 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073949/0 /scratch/stefan/7916156/working/building/REAL250005073949 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 56) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/56 `/scratch/stefan/7916156/working/3D/56' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC12CC1CN(C(=O)C1=CC(=O)[N-]O1)C2) `REAL250005073949.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073949.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073949/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073949 none CC(=O)NCC12CC1CN(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [97, 97, 97, 76, 27, 27, 27, 27, 27, 10, 1, 10, 1, 1, 1, 1, 1, 1, 27, 97, 97, 97, 97, 76, 76, 27, 27, 27, 27, 27, 1, 27, 27] 97 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: 320 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073949 none CC(=O)NCC12CC1CN(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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: [43, 43, 43, 10, 1, 1, 1, 1, 1, 1, 1, 6, 6, 27, 27, 27, 27, 27, 1, 43, 43, 43, 43, 10, 10, 1, 1, 1, 1, 1, 27, 1, 1] 97 rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 10, 18, 25, 26, 27, 28, 29, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 30]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073949 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073949 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073949/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073949 Building REAL250005073950 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073950' /scratch/stefan/7916156/working/building/REAL250005073950 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073950 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073950/0 /scratch/stefan/7916156/working/building/REAL250005073950 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 57) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/57 `/scratch/stefan/7916156/working/3D/57' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC12CC1CN(C(=O)C1=CC(=O)[N-]O1)C2)C1CC1) `REAL250005073950.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073950/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073950 none O=C(NCC12CC1CN(C(=O)C1=CC(=O)[N-]O1)C2)C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [140, 140, 67, 18, 18, 18, 18, 18, 7, 1, 7, 1, 1, 1, 1, 1, 1, 18, 140, 201, 201, 140, 67, 67, 18, 18, 18, 18, 18, 1, 18, 18, 201, 201, 201, 201, 201] 201 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 660 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073950 none O=C(NCC12CC1CN(C(=O)C1=CC(=O)[N-]O1)C2)C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [47, 47, 10, 1, 1, 1, 1, 1, 1, 1, 6, 6, 18, 18, 18, 18, 18, 1, 47, 137, 137, 47, 10, 10, 1, 1, 1, 1, 1, 18, 1, 1, 137, 137, 137, 137, 137] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 17, 24, 25, 26, 27, 28, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 29, 32, 33, 34, 35, 36]) total number of confs: 397 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.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: REAL250005073950 none O=C(NCC12CC1CN(C(=O)C1=CC(=O)[N-]O1)C2)C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 54, 137, 137, 137, 137, 137, 200, 200, 201, 201, 201, 201, 201, 137, 1, 1, 1, 11, 54, 54, 137, 137, 137, 137, 137, 201, 137, 137, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 34, 35, 36, 33, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 520 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073950 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073950 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073950/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073950 Building REAL250005073951 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073951' /scratch/stefan/7916156/working/building/REAL250005073951 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073951 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073951/0 /scratch/stefan/7916156/working/building/REAL250005073951 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 58) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/58 `/scratch/stefan/7916156/working/3D/58' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)NCC12CC1CN(C(=O)C1=CC(=O)[N-]O1)C2) `REAL250005073951.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073951/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073951 none COCC(=O)NCC12CC1CN(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 144, 144, 144, 60, 18, 18, 18, 18, 18, 6, 1, 6, 1, 1, 1, 1, 1, 1, 18, 201, 201, 201, 201, 201, 144, 60, 60, 18, 18, 18, 18, 18, 1, 18, 18] 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: 726 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073951 none COCC(=O)NCC12CC1CN(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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: [153, 134, 46, 46, 46, 10, 1, 1, 1, 1, 1, 1, 1, 6, 6, 18, 18, 18, 18, 18, 1, 153, 153, 153, 134, 134, 46, 10, 10, 1, 1, 1, 1, 1, 18, 1, 1] 201 rigid atoms, others: [32, 33, 35, 36, 6, 7, 8, 9, 10, 11, 12, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 34]) total number of confs: 547 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073951 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073951 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073951/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073951 Building REAL250005073952 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073952' /scratch/stefan/7916156/working/building/REAL250005073952 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073952 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073952/0 /scratch/stefan/7916156/working/building/REAL250005073952 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 59) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/59 `/scratch/stefan/7916156/working/3D/59' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)NCC12CC1CN(C(=O)C1=CC(=O)[N-]O1)C2) `REAL250005073952.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073952/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073952 none CCCC(=O)NCC12CC1CN(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 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, 199, 116, 116, 116, 45, 14, 14, 14, 14, 14, 6, 1, 6, 1, 1, 1, 1, 1, 1, 14, 201, 201, 201, 201, 201, 199, 199, 116, 45, 45, 14, 14, 14, 14, 14, 1, 14, 14] 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: 780 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073952 none CCCC(=O)NCC12CC1CN(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 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: [149, 138, 39, 39, 39, 9, 1, 1, 1, 1, 1, 1, 1, 5, 5, 14, 14, 14, 14, 14, 1, 160, 160, 160, 160, 160, 138, 138, 39, 9, 9, 1, 1, 1, 1, 1, 14, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 37, 6, 7, 8, 9, 10, 11, 12, 20, 38, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36]) total number of confs: 711 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073952 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073952 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073952/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073952 Building REAL250005073953 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073953' /scratch/stefan/7916156/working/building/REAL250005073953 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073953 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073953/0 /scratch/stefan/7916156/working/building/REAL250005073953 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 60) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/60 `/scratch/stefan/7916156/working/3D/60' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)NCC12CC1CN(C(=O)C1=CC(=O)[N-]O1)C2) `REAL250005073953.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073953.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073953/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073953 none CC(C)C(=O)NCC12CC1CN(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 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, 171, 201, 171, 171, 84, 24, 24, 24, 24, 24, 9, 1, 9, 1, 1, 1, 1, 1, 1, 24, 201, 201, 201, 201, 201, 201, 201, 171, 84, 84, 24, 24, 24, 24, 24, 1, 24, 24] 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: 722 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073953 none CC(C)C(=O)NCC12CC1CN(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 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: [132, 51, 132, 51, 51, 10, 1, 1, 1, 1, 1, 1, 1, 6, 6, 24, 24, 24, 24, 24, 1, 132, 132, 132, 132, 132, 132, 132, 51, 10, 10, 1, 1, 1, 1, 1, 24, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 37, 6, 7, 8, 9, 10, 11, 12, 20, 38, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36]) total number of confs: 521 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073953 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073953 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073953/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073953 Building REAL250005073954 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073954' /scratch/stefan/7916156/working/building/REAL250005073954 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073954 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073954/0 /scratch/stefan/7916156/working/building/REAL250005073954 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 61) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/61 `/scratch/stefan/7916156/working/3D/61' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C(=O)NCC12CC1CN(C(=O)C1=CC(=O)[N-]O1)C2) `REAL250005073954.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073954/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073954 none NC(=O)C(=O)NCC12CC1CN(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 198, 201, 198, 198, 105, 27, 27, 27, 27, 27, 10, 1, 10, 1, 1, 1, 1, 1, 1, 27, 201, 201, 198, 105, 105, 27, 27, 27, 27, 27, 1, 27, 27] 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, 32, 33]) total number of confs: 640 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073954 none NC(=O)C(=O)NCC12CC1CN(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 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: [94, 54, 94, 54, 54, 10, 1, 1, 1, 1, 1, 1, 1, 6, 6, 27, 27, 27, 27, 27, 1, 94, 94, 54, 10, 10, 1, 1, 1, 1, 1, 27, 1, 1] 201 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 12, 20, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 31]) total number of confs: 314 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073954 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073954 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073954/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073954 Building REAL250005073955 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073955' /scratch/stefan/7916156/working/building/REAL250005073955 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073955 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073955/0 /scratch/stefan/7916156/working/building/REAL250005073955 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 62) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/62 `/scratch/stefan/7916156/working/3D/62' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(=O)NCC12CC1CN(C(=O)C1=CC(=O)[N-]O1)C2) `REAL250005073955.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073955/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073955 none C=CCC(=O)NCC12CC1CN(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 128, 128, 128, 52, 13, 13, 13, 13, 13, 8, 1, 8, 1, 1, 1, 1, 1, 1, 13, 201, 201, 201, 201, 201, 128, 52, 52, 13, 13, 13, 13, 13, 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: 759 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073955 none C=CCC(=O)NCC12CC1CN(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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: [164, 139, 40, 40, 40, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 13, 13, 13, 13, 13, 1, 164, 164, 164, 139, 139, 40, 10, 10, 1, 1, 1, 1, 1, 13, 1, 1] 201 rigid atoms, others: [32, 33, 35, 36, 6, 7, 8, 9, 10, 11, 12, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 34]) total number of confs: 606 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073955 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073955 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073955/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073955 Building REAL250005073956 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073956' /scratch/stefan/7916156/working/building/REAL250005073956 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073956 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073956/0 /scratch/stefan/7916156/working/building/REAL250005073956 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 63) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/63 `/scratch/stefan/7916156/working/3D/63' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CO)NCC12CC1CN(C(=O)C1=CC(=O)[N-]O1)C2) `REAL250005073956.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073956.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073956/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073956 none O=C(CO)NCC12CC1CN(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 528 conformations in input total number of sets (complete confs): 528 using faster count positions algorithm for large data unique positions, atoms: [176, 176, 176, 176, 105, 28, 28, 28, 28, 28, 10, 1, 10, 1, 1, 1, 1, 1, 1, 28, 176, 176, 528, 176, 105, 105, 28, 28, 28, 28, 28, 1, 28, 28] 528 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33]) total number of confs: 1095 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073956 none O=C(CO)NCC12CC1CN(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 528 conformations in input total number of sets (complete confs): 528 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 51, 103, 10, 1, 1, 1, 1, 1, 1, 1, 6, 6, 28, 28, 28, 28, 28, 1, 103, 103, 309, 51, 10, 10, 1, 1, 1, 1, 1, 28, 1, 1] 528 rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 11, 19, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 31]) total number of confs: 714 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073956 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073956 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073956/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073956 Building REAL250005073957 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073957' /scratch/stefan/7916156/working/building/REAL250005073957 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073957 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073957/0 /scratch/stefan/7916156/working/building/REAL250005073957 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 64) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/64 `/scratch/stefan/7916156/working/3D/64' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)C(=O)NCC12CC1CN(C(=O)C1=CC(=O)[N-]O1)C2) `REAL250005073957.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073957.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073957/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073957 none CC(O)C(=O)NCC12CC1CN(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [201, 189, 201, 189, 189, 98, 24, 24, 24, 24, 24, 9, 1, 9, 1, 1, 1, 1, 1, 1, 24, 201, 201, 201, 201, 603, 189, 98, 98, 24, 24, 24, 24, 24, 1, 24, 24] 603 rigid atoms, others: [34, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36]) total number of confs: 1287 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073957 none CC(O)C(=O)NCC12CC1CN(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 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: [142, 54, 142, 54, 54, 10, 1, 1, 1, 1, 1, 1, 1, 6, 6, 24, 24, 24, 24, 24, 1, 142, 142, 142, 142, 426, 54, 10, 10, 1, 1, 1, 1, 1, 24, 1, 1] 603 rigid atoms, others: [32, 33, 35, 36, 6, 7, 8, 9, 10, 11, 12, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 34]) total number of confs: 983 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073957 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073957 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073957/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073957 Building REAL250005073958 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073958' /scratch/stefan/7916156/working/building/REAL250005073958 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073958 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073958/0 /scratch/stefan/7916156/working/building/REAL250005073958 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 65) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/65 `/scratch/stefan/7916156/working/3D/65' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCF)NCC12CC1CN(C(=O)C1=CC(=O)[N-]O1)C2) `REAL250005073958.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073958/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073958 none O=C(CCF)NCC12CC1CN(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 15, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [108, 108, 108, 201, 201, 42, 14, 14, 14, 14, 14, 5, 1, 5, 1, 1, 1, 1, 1, 1, 14, 201, 201, 201, 201, 108, 42, 42, 14, 14, 14, 14, 14, 1, 14, 14] 201 rigid atoms, others: [33, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35]) total number of confs: 748 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073958 none O=C(CCF)NCC12CC1CN(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 15, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 40, 40, 143, 161, 10, 1, 1, 1, 1, 1, 1, 1, 6, 6, 14, 14, 14, 14, 14, 1, 143, 143, 161, 161, 40, 10, 10, 1, 1, 1, 1, 1, 14, 1, 1] 201 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 12, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 33, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 635 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073958 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073958 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073958/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073958 Building REAL250005073959 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073959' /scratch/stefan/7916156/working/building/REAL250005073959 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073959 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073959/0 /scratch/stefan/7916156/working/building/REAL250005073959 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 66) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/66 `/scratch/stefan/7916156/working/3D/66' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)C(=O)NCC12CC1CN(C(=O)C1=CC(=O)[N-]O1)C2) `REAL250005073959.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073959/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073959 none C[C@@H](O)C(=O)NCC12CC1CN(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 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, 181, 201, 201, 181, 181, 96, 26, 26, 26, 26, 26, 10, 1, 10, 1, 1, 1, 1, 1, 1, 26, 201, 201, 201, 603, 181, 96, 96, 26, 26, 26, 26, 26, 1, 26, 26] 603 rigid atoms, others: [34, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36]) total number of confs: 1289 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073959 none C[C@@H](O)C(=O)NCC12CC1CN(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 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: [142, 54, 142, 139, 54, 54, 10, 1, 1, 1, 1, 1, 1, 1, 6, 6, 26, 26, 26, 26, 26, 1, 142, 142, 142, 426, 54, 10, 10, 1, 1, 1, 1, 1, 26, 1, 1] 603 rigid atoms, others: [32, 33, 35, 36, 7, 8, 9, 10, 11, 12, 13, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 34]) total number of confs: 983 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073959 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073959 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073959/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073959 Building REAL250005073960 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073960' /scratch/stefan/7916156/working/building/REAL250005073960 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073960 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073960/0 /scratch/stefan/7916156/working/building/REAL250005073960 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 67) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/67 `/scratch/stefan/7916156/working/3D/67' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)C(=O)NCC12CC1CN(C(=O)C1=CC(=O)[N-]O1)C2) `REAL250005073960.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073960.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073960/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073960 none C[C@H](O)C(=O)NCC12CC1CN(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 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, 189, 201, 201, 189, 189, 97, 24, 24, 24, 24, 24, 9, 1, 9, 1, 1, 1, 1, 1, 1, 24, 201, 201, 201, 603, 189, 97, 97, 24, 24, 24, 24, 24, 1, 24, 24] 603 rigid atoms, others: [34, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36]) total number of confs: 1288 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073960 none C[C@H](O)C(=O)NCC12CC1CN(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 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: [140, 54, 140, 137, 54, 54, 10, 1, 1, 1, 1, 1, 1, 1, 6, 6, 24, 24, 24, 24, 24, 1, 140, 140, 140, 420, 54, 10, 10, 1, 1, 1, 1, 1, 24, 1, 1] 603 rigid atoms, others: [32, 33, 35, 36, 7, 8, 9, 10, 11, 12, 13, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 34]) total number of confs: 965 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073960 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073960 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073960/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073960 Building REAL250005073961 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073961' /scratch/stefan/7916156/working/building/REAL250005073961 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073961 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073961/0 /scratch/stefan/7916156/working/building/REAL250005073961 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 68) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/68 `/scratch/stefan/7916156/working/3D/68' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC(=O)NCC12CC1CN(C(=O)C1=CC(=O)[N-]O1)C2) `REAL250005073961.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073961/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073961 none CC=CC(=O)NCC12CC1CN(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 174, 174, 174, 86, 24, 24, 24, 24, 24, 9, 1, 9, 1, 1, 1, 1, 1, 1, 24, 201, 201, 201, 201, 201, 174, 86, 86, 24, 24, 24, 24, 24, 1, 24, 24] 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: 653 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073961 none CC=CC(=O)NCC12CC1CN(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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: [132, 132, 55, 55, 55, 10, 1, 1, 1, 1, 1, 1, 1, 6, 6, 24, 24, 24, 24, 24, 1, 132, 132, 132, 132, 132, 55, 10, 10, 1, 1, 1, 1, 1, 24, 1, 1] 201 rigid atoms, others: [32, 33, 35, 36, 6, 7, 8, 9, 10, 11, 12, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 34]) total number of confs: 401 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073961 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073961 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073961/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073961 Building REAL250005073962 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073962' /scratch/stefan/7916156/working/building/REAL250005073962 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073962 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073962/0 /scratch/stefan/7916156/working/building/REAL250005073962 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 69) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/69 `/scratch/stefan/7916156/working/3D/69' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)N1CC2CC2(CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005073962.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073962.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073962/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073962 none COCC(=O)N1CC2CC2(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 190, 110, 71, 110, 71, 71, 71, 71, 20, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 71, 201, 201, 201, 190, 190, 71, 71, 71, 71, 71, 20, 20, 4, 1, 71, 71] 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: 680 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073962 none COCC(=O)N1CC2CC2(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [57, 23, 6, 1, 6, 1, 1, 1, 1, 1, 1, 10, 53, 53, 53, 71, 71, 71, 71, 71, 1, 57, 57, 57, 23, 23, 1, 1, 1, 1, 1, 10, 10, 53, 71, 1, 1] 201 rigid atoms, others: [3, 36, 5, 6, 7, 8, 9, 10, 35, 20, 26, 27, 28, 29, 30] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 31, 32, 33, 34]) total number of confs: 292 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073962 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073962 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073962/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073962 Building REAL250005073963 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073963' /scratch/stefan/7916156/working/building/REAL250005073963 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073963 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073963/0 /scratch/stefan/7916156/working/building/REAL250005073963 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 70) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/70 `/scratch/stefan/7916156/working/3D/70' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)N1CC2CC2(CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005073963.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073963/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073963 none CCCC(=O)N1CC2CC2(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 118, 69, 118, 69, 69, 69, 69, 18, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 69, 201, 201, 201, 201, 201, 198, 198, 69, 69, 69, 69, 69, 18, 18, 4, 1, 69, 69] 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: 698 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073963 none CCCC(=O)N1CC2CC2(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 7, 1, 7, 1, 1, 1, 1, 1, 1, 10, 56, 56, 56, 69, 69, 69, 69, 69, 1, 33, 33, 33, 33, 33, 23, 23, 1, 1, 1, 1, 1, 10, 10, 56, 69, 1, 1] 201 rigid atoms, others: [32, 3, 5, 6, 7, 8, 9, 10, 37, 20, 38, 28, 29, 30, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35, 36]) total number of confs: 322 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073963 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073963 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073963/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073963 Building REAL250005073964 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073964' /scratch/stefan/7916156/working/building/REAL250005073964 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073964 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073964/0 /scratch/stefan/7916156/working/building/REAL250005073964 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 71) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/71 `/scratch/stefan/7916156/working/3D/71' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N1CC2CC2(CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005073964.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073964/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073964 none CC(C)C(=O)N1CC2CC2(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 116, 119, 73, 116, 73, 73, 73, 73, 25, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 73, 119, 119, 119, 119, 119, 119, 119, 73, 73, 73, 73, 73, 25, 25, 8, 1, 73, 73] 119 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: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073964 none CC(C)C(=O)N1CC2CC2(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [18, 7, 18, 1, 7, 1, 1, 1, 1, 1, 1, 10, 52, 52, 52, 73, 73, 73, 73, 73, 1, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1, 1, 10, 10, 52, 73, 1, 1] 119 rigid atoms, others: [32, 3, 5, 6, 7, 8, 9, 10, 37, 20, 38, 28, 29, 30, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35, 36]) total number of confs: 235 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073964 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073964 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073964/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073964 Building REAL250005073965 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073965' /scratch/stefan/7916156/working/building/REAL250005073965 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073965 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073965/0 /scratch/stefan/7916156/working/building/REAL250005073965 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 72) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/72 `/scratch/stefan/7916156/working/3D/72' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N1CC2CC2(CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005073965.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073965/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073965 none CCC(=O)N1CC2CC2(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 146, 97, 146, 97, 97, 97, 97, 33, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 97, 149, 149, 149, 149, 149, 97, 97, 97, 97, 97, 33, 33, 9, 1, 97, 97] 149 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: 381 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073965 none CCC(=O)N1CC2CC2(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [22, 7, 1, 7, 1, 1, 1, 1, 1, 1, 10, 58, 58, 58, 97, 97, 97, 97, 97, 1, 22, 22, 22, 22, 22, 1, 1, 1, 1, 1, 10, 10, 58, 97, 1, 1] 149 rigid atoms, others: [2, 35, 4, 5, 6, 7, 8, 9, 34, 19, 25, 26, 27, 28, 29] set([0, 1, 3, 33, 32, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 30, 31]) total number of confs: 287 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073965 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073965 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073965/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073965 Building REAL250005073966 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073966' /scratch/stefan/7916156/working/building/REAL250005073966 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073966 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073966/0 /scratch/stefan/7916156/working/building/REAL250005073966 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 73) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/73 `/scratch/stefan/7916156/working/3D/73' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC2CC2(CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005073966.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073966/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073966 none CC(=O)N1CC2CC2(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [57, 42, 57, 42, 42, 42, 42, 24, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 42, 57, 57, 57, 42, 42, 42, 42, 42, 24, 24, 6, 1, 42, 42] 57 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: 169 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073966 none CC(=O)N1CC2CC2(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 1, 1, 1, 1, 1, 1, 10, 36, 36, 36, 42, 42, 42, 42, 42, 1, 6, 6, 6, 1, 1, 1, 1, 1, 10, 10, 36, 42, 1, 1] 57 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 18, 22, 23, 24, 25, 26, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 27, 28, 29, 30]) total number of confs: 124 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073966 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073966 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073966/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073966 Building REAL250005073967 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073967' /scratch/stefan/7916156/working/building/REAL250005073967 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073967 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073967/0 /scratch/stefan/7916156/working/building/REAL250005073967 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 74) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/74 `/scratch/stefan/7916156/working/3D/74' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC12CC1CN(C(=O)C1CC1)C2)C1=CC(=O)[N-]O1) `REAL250005073967.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073967.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073967/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073967 none O=C(NCC12CC1CN(C(=O)C1CC1)C2)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 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, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 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, 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: [153, 153, 72, 26, 26, 26, 26, 26, 8, 1, 8, 1, 1, 1, 26, 153, 158, 158, 158, 158, 158, 153, 72, 72, 26, 26, 26, 26, 26, 1, 1, 1, 1, 1, 26, 26, 158] 158 rigid atoms, others: [32, 33, 9, 11, 12, 13, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36]) total number of confs: 470 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073967 none O=C(NCC12CC1CN(C(=O)C1CC1)C2)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 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, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 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, 7, 7] 0 hydrogens need rotated 158 conformations in input total number of sets (complete confs): 158 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 10, 1, 1, 1, 1, 1, 1, 1, 6, 6, 26, 26, 1, 54, 81, 81, 81, 81, 81, 54, 10, 10, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 1, 1, 81] 158 rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 9, 14, 35, 24, 25, 26, 27, 28] set([0, 1, 2, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 36]) total number of confs: 248 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.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: REAL250005073967 none O=C(NCC12CC1CN(C(=O)C1CC1)C2)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 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, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 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, 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: [7, 1, 7, 7, 31, 81, 81, 81, 81, 81, 106, 106, 158, 158, 81, 1, 1, 1, 1, 1, 1, 7, 31, 31, 81, 81, 81, 81, 81, 158, 158, 158, 158, 158, 81, 81, 1] 158 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: 477 number of broken/clashed sets: 6 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073967 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073967 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073967/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073967 Building REAL250005073968 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073968' /scratch/stefan/7916156/working/building/REAL250005073968 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073968 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073968/0 /scratch/stefan/7916156/working/building/REAL250005073968 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 75) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/75 `/scratch/stefan/7916156/working/3D/75' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C(=O)N1CC2CC2(CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005073968.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073968.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073968/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073968 none NC(=O)C(=O)N1CC2CC2(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [4, 7, 6, 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 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [49, 34, 49, 29, 34, 29, 29, 29, 29, 16, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 29, 49, 49, 29, 29, 29, 29, 29, 16, 16, 6, 1, 29, 29] 49 rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33]) total number of confs: 148 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073968 none NC(=O)C(=O)N1CC2CC2(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [4, 7, 6, 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 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [16, 4, 16, 1, 4, 1, 1, 1, 1, 1, 1, 7, 24, 24, 24, 29, 29, 29, 29, 29, 1, 16, 16, 1, 1, 1, 1, 1, 7, 7, 24, 29, 1, 1] 49 rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 10, 20, 23, 24, 25, 26, 27] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 28, 29, 30, 31]) total number of confs: 113 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073968 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073968 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073968/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073968 Building REAL250005073969 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073969' /scratch/stefan/7916156/working/building/REAL250005073969 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073969 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073969/0 /scratch/stefan/7916156/working/building/REAL250005073969 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 76) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/76 `/scratch/stefan/7916156/working/3D/76' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CO)N1CC2CC2(CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005073969.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073969/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073969 none O=C(CO)N1CC2CC2(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 312 conformations in input total number of sets (complete confs): 312 using faster count positions algorithm for large data unique positions, atoms: [93, 62, 93, 104, 62, 62, 62, 62, 20, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 62, 104, 104, 312, 62, 62, 62, 62, 62, 20, 20, 8, 1, 62, 62] 312 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33]) total number of confs: 612 number of broken/clashed sets: 28 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073969 none O=C(CO)N1CC2CC2(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 312 conformations in input total number of sets (complete confs): 312 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 17, 1, 1, 1, 1, 1, 1, 10, 51, 51, 51, 62, 62, 62, 62, 62, 1, 17, 17, 51, 1, 1, 1, 1, 1, 10, 10, 51, 62, 1, 1] 312 rigid atoms, others: [32, 1, 33, 4, 5, 6, 7, 8, 9, 19, 23, 24, 25, 26, 27] set([0, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 28, 29, 30, 31]) total number of confs: 258 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073969 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073969 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073969/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073969 Building REAL250005073970 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073970' /scratch/stefan/7916156/working/building/REAL250005073970 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073970 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073970/0 /scratch/stefan/7916156/working/building/REAL250005073970 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 77) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/77 `/scratch/stefan/7916156/working/3D/77' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)C(=O)N1CC2CC2(CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005073970.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073970/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073970 none CC(O)C(=O)N1CC2CC2(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [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] 1 hydrogens need rotated 303 conformations in input total number of sets (complete confs): 303 using faster count positions algorithm for large data unique positions, atoms: [101, 60, 101, 50, 60, 50, 50, 50, 50, 18, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 50, 101, 101, 101, 101, 303, 50, 50, 50, 50, 50, 18, 18, 7, 1, 50, 50] 303 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: 647 number of broken/clashed sets: 38 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073970 none CC(O)C(=O)N1CC2CC2(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [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] 1 hydrogens need rotated 303 conformations in input total number of sets (complete confs): 303 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 13, 1, 5, 1, 1, 1, 1, 1, 1, 10, 40, 40, 40, 50, 50, 50, 50, 50, 1, 13, 13, 13, 13, 39, 1, 1, 1, 1, 1, 10, 10, 40, 50, 1, 1] 303 rigid atoms, others: [3, 36, 5, 6, 7, 8, 9, 10, 35, 20, 26, 27, 28, 29, 30] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 31, 32, 33, 34]) total number of confs: 207 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073970 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073970 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073970/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073970 Building REAL250005073971 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073971' /scratch/stefan/7916156/working/building/REAL250005073971 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073971 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073971/0 /scratch/stefan/7916156/working/building/REAL250005073971 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 78) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/78 `/scratch/stefan/7916156/working/3D/78' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)C(=O)N1CC2CC2(CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005073971.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073971/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073971 none CC(=O)C(=O)N1CC2CC2(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 11, 8, 5, 5, 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, 3, 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 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [78, 65, 78, 52, 65, 52, 52, 52, 52, 18, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 52, 78, 78, 78, 52, 52, 52, 52, 52, 18, 18, 6, 1, 52, 52] 78 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: 206 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073971 none CC(=O)C(=O)N1CC2CC2(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 11, 8, 5, 5, 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, 3, 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 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [16, 5, 16, 1, 5, 1, 1, 1, 1, 1, 1, 9, 41, 41, 41, 52, 52, 52, 52, 52, 1, 16, 16, 16, 1, 1, 1, 1, 1, 9, 9, 41, 52, 1, 1] 78 rigid atoms, others: [33, 34, 3, 5, 6, 7, 8, 9, 10, 20, 24, 25, 26, 27, 28] set([0, 1, 2, 4, 32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 29, 30, 31]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073971 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073971 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073971/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073971 Building REAL250005073972 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073972' /scratch/stefan/7916156/working/building/REAL250005073972 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073972 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073972/0 /scratch/stefan/7916156/working/building/REAL250005073972 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 79) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/79 `/scratch/stefan/7916156/working/3D/79' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC(=O)N1CC2CC2(CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005073972.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073972/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073972 none CC=CC(=O)N1CC2CC2(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [147, 147, 122, 76, 122, 76, 76, 76, 76, 26, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 76, 147, 147, 147, 147, 147, 76, 76, 76, 76, 76, 26, 26, 7, 1, 76, 76] 147 rigid atoms, others: [34, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36]) total number of confs: 405 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073972 none CC=CC(=O)N1CC2CC2(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 7, 1, 7, 1, 1, 1, 1, 1, 1, 10, 54, 54, 54, 76, 76, 76, 76, 76, 1, 32, 32, 32, 32, 32, 1, 1, 1, 1, 1, 10, 10, 54, 76, 1, 1] 147 rigid atoms, others: [3, 36, 5, 6, 7, 8, 9, 10, 35, 20, 26, 27, 28, 29, 30] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 31, 32, 33, 34]) total number of confs: 254 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073972 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073972 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073972/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073972 Building REAL250005073973 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073973' /scratch/stefan/7916156/working/building/REAL250005073973 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073973 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073973/0 /scratch/stefan/7916156/working/building/REAL250005073973 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 80) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/80 `/scratch/stefan/7916156/working/3D/80' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)C(=O)N1CC2CC2(CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005073973.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073973/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073973 none C[C@H](O)C(=O)N1CC2CC2(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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] 1 hydrogens need rotated 297 conformations in input total number of sets (complete confs): 297 using faster count positions algorithm for large data unique positions, atoms: [99, 57, 99, 99, 48, 57, 48, 48, 48, 48, 17, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 48, 99, 99, 99, 297, 48, 48, 48, 48, 48, 17, 17, 6, 1, 48, 48] 297 rigid atoms, others: [34, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36]) total number of confs: 642 number of broken/clashed sets: 36 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073973 none C[C@H](O)C(=O)N1CC2CC2(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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] 1 hydrogens need rotated 297 conformations in input total number of sets (complete confs): 297 using faster count positions algorithm for large data unique positions, atoms: [14, 5, 14, 14, 1, 5, 1, 1, 1, 1, 1, 1, 9, 40, 40, 40, 48, 48, 48, 48, 48, 1, 14, 14, 14, 42, 1, 1, 1, 1, 1, 9, 9, 40, 48, 1, 1] 297 rigid atoms, others: [35, 4, 6, 7, 8, 9, 10, 11, 21, 36, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 31, 32, 33, 34]) total number of confs: 209 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073973 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073973 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073973/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073973 Building REAL250005073974 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073974' /scratch/stefan/7916156/working/building/REAL250005073974 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073974 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073974/0 /scratch/stefan/7916156/working/building/REAL250005073974 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 81) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/81 `/scratch/stefan/7916156/working/3D/81' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(=O)N1CC2CC2(CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005073974.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073974/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073974 none C=CCC(=O)N1CC2CC2(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 70, 116, 70, 70, 70, 70, 18, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 70, 201, 201, 201, 201, 201, 70, 70, 70, 70, 70, 18, 18, 4, 1, 70, 70] 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: 711 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073974 none C=CCC(=O)N1CC2CC2(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [56, 26, 7, 1, 7, 1, 1, 1, 1, 1, 1, 10, 56, 56, 56, 70, 70, 70, 70, 70, 1, 56, 56, 56, 26, 26, 1, 1, 1, 1, 1, 10, 10, 56, 70, 1, 1] 201 rigid atoms, others: [3, 36, 5, 6, 7, 8, 9, 10, 35, 20, 26, 27, 28, 29, 30] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 31, 32, 33, 34]) total number of confs: 343 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073974 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073974 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073974/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073974 Building REAL250005073975 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073975' /scratch/stefan/7916156/working/building/REAL250005073975 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073975 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073975/0 /scratch/stefan/7916156/working/building/REAL250005073975 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 82) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/82 `/scratch/stefan/7916156/working/3D/82' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCC(=O)N1CC2CC2(CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005073975.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073975/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073975 none N#CCC(=O)N1CC2CC2(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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, 124, 80, 124, 80, 80, 80, 80, 24, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 80, 189, 189, 80, 80, 80, 80, 80, 24, 24, 9, 1, 80, 80] 189 rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33]) total number of confs: 637 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073975 none N#CCC(=O)N1CC2CC2(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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: [32, 32, 6, 1, 6, 1, 1, 1, 1, 1, 1, 10, 55, 55, 55, 80, 80, 80, 80, 80, 1, 32, 32, 1, 1, 1, 1, 1, 10, 10, 55, 80, 1, 1] 189 rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 10, 20, 23, 24, 25, 26, 27] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 28, 29, 30, 31]) total number of confs: 290 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073975 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073975 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073975/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073975 Building REAL250005073976 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073976' /scratch/stefan/7916156/working/building/REAL250005073976 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073976 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073976/0 /scratch/stefan/7916156/working/building/REAL250005073976 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 83) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/83 `/scratch/stefan/7916156/working/3D/83' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCF)N1CC2CC2(CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005073976.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073976/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073976 none O=C(CCF)N1CC2CC2(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 15, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [97, 60, 97, 201, 201, 60, 60, 60, 60, 15, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 60, 201, 201, 201, 201, 60, 60, 60, 60, 60, 15, 15, 4, 1, 60, 60] 201 rigid atoms, others: [33, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35]) total number of confs: 736 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073976 none O=C(CCF)N1CC2CC2(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 15, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 16, 29, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 60, 60, 60, 60, 60, 1, 16, 16, 29, 29, 1, 1, 1, 1, 1, 10, 10, 50, 60, 1, 1] 201 rigid atoms, others: [1, 34, 35, 5, 6, 7, 8, 9, 10, 20, 25, 26, 27, 28, 29] set([0, 32, 2, 3, 4, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 30, 31]) total number of confs: 268 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073976 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073976 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073976/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073976 Building REAL250005073977 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073977' /scratch/stefan/7916156/working/building/REAL250005073977 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073977 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073977/0 /scratch/stefan/7916156/working/building/REAL250005073977 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 84) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/84 `/scratch/stefan/7916156/working/3D/84' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)C(=O)N1CC2CC2(CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005073977.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073977/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073977 none C[C@@H](O)C(=O)N1CC2CC2(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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] 1 hydrogens need rotated 303 conformations in input total number of sets (complete confs): 303 using faster count positions algorithm for large data unique positions, atoms: [101, 60, 101, 101, 50, 60, 50, 50, 50, 50, 18, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 50, 101, 101, 101, 303, 50, 50, 50, 50, 50, 18, 18, 7, 1, 50, 50] 303 rigid atoms, others: [34, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36]) total number of confs: 647 number of broken/clashed sets: 38 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073977 none C[C@@H](O)C(=O)N1CC2CC2(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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] 1 hydrogens need rotated 303 conformations in input total number of sets (complete confs): 303 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 13, 13, 1, 5, 1, 1, 1, 1, 1, 1, 10, 40, 40, 40, 50, 50, 50, 50, 50, 1, 13, 13, 13, 39, 1, 1, 1, 1, 1, 10, 10, 40, 50, 1, 1] 303 rigid atoms, others: [35, 4, 6, 7, 8, 9, 10, 11, 21, 36, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 31, 32, 33, 34]) total number of confs: 207 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073977 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073977 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073977/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073977 Building REAL250005073978 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073978' /scratch/stefan/7916156/working/building/REAL250005073978 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073978 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073978/0 /scratch/stefan/7916156/working/building/REAL250005073978 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 85) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/85 `/scratch/stefan/7916156/working/3D/85' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(=O)N1CC2CC2(CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005073978.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073978/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073978 none C=CC(=O)N1CC2CC2(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 5, 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, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 113 conformations in input total number of sets (complete confs): 113 using faster count positions algorithm for large data unique positions, atoms: [113, 113, 82, 113, 82, 82, 82, 82, 28, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 82, 113, 113, 113, 82, 82, 82, 82, 82, 28, 28, 7, 1, 82, 82] 113 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33]) total number of confs: 275 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073978 none C=CC(=O)N1CC2CC2(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 5, 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, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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: [26, 7, 1, 7, 1, 1, 1, 1, 1, 1, 10, 55, 55, 55, 82, 82, 82, 82, 82, 1, 26, 26, 26, 1, 1, 1, 1, 1, 10, 10, 55, 82, 1, 1] 113 rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 9, 19, 23, 24, 25, 26, 27] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 28, 29, 30, 31]) total number of confs: 248 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073978 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073978 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073978/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073978 Building REAL250005073979 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073979' /scratch/stefan/7916156/working/building/REAL250005073979 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073979 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073979/0 /scratch/stefan/7916156/working/building/REAL250005073979 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 86) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/86 `/scratch/stefan/7916156/working/3D/86' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC(C)(C)C1CCN(C(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005073979.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073979/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073979 none CC(=O)NC(C)(C)C1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 55, 37, 19, 37, 37, 19, 19, 19, 11, 1, 11, 1, 1, 1, 1, 1, 1, 19, 19, 55, 55, 55, 55, 37, 37, 37, 37, 37, 37, 19, 19, 19, 19, 19, 1, 19, 19, 19, 19] 55 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: 193 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073979 none CC(=O)NC(C)(C)C1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 4, 1, 4, 4, 1, 1, 1, 1, 1, 7, 7, 19, 19, 19, 19, 19, 1, 1, 6, 6, 6, 6, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 19, 1, 1, 1, 1] 55 rigid atoms, others: [32, 33, 34, 35, 4, 37, 38, 7, 8, 9, 10, 11, 40, 19, 20, 39, 31] set([0, 1, 2, 3, 5, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073979 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073979 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073979/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073979 Building REAL250005073980 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073980' /scratch/stefan/7916156/working/building/REAL250005073980 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073980 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073980/0 /scratch/stefan/7916156/working/building/REAL250005073980 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 87) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/87 `/scratch/stefan/7916156/working/3D/87' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC(C(C)(C)NC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005073980.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073980/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073980 none CC(=O)N1CCC(C(C)(C)NC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 24, 37, 24, 24, 24, 16, 7, 16, 16, 7, 1, 7, 1, 1, 1, 1, 1, 1, 24, 24, 37, 37, 37, 24, 24, 24, 24, 24, 16, 16, 16, 16, 16, 16, 7, 1, 24, 24, 24, 24] 37 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: 134 number of broken/clashed sets: 19 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073980 none CC(=O)N1CCC(C(C)(C)NC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 1, 1, 1, 1, 1, 8, 8, 8, 12, 12, 12, 24, 24, 24, 24, 24, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 12, 24, 1, 1, 1, 1] 37 rigid atoms, others: [1, 3, 4, 5, 6, 7, 38, 39, 40, 19, 20, 24, 25, 26, 27, 28, 37] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 68 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073980 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073980 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073980/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073980 Building REAL250005073981 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073981' /scratch/stefan/7916156/working/building/REAL250005073981 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073981 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073981/0 /scratch/stefan/7916156/working/building/REAL250005073981 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 88) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/88 `/scratch/stefan/7916156/working/3D/88' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NC12CC1CN(C(=O)C1=CC(=O)[N-]O1)CCC2) `REAL250005073981.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073981/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073981 none CCC(=O)NC12CC1CN(C(=O)C1=CC(=O)[N-]O1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [40, 23, 23, 23, 23, 23, 23, 23, 23, 9, 1, 9, 1, 1, 1, 1, 1, 1, 23, 23, 23, 40, 40, 40, 40, 40, 23, 23, 23, 23, 23, 23, 1, 23, 23, 23, 23, 23, 23] 40 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: 143 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073981 none CCC(=O)NC12CC1CN(C(=O)C1=CC(=O)[N-]O1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 7, 7, 23, 23, 23, 23, 23, 1, 1, 1, 7, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 23, 1, 1, 1, 1, 1, 1] 40 rigid atoms, others: [33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 37, 18, 19, 20, 38, 36, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 32, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073981 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073981 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073981/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073981 Building REAL250005073982 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073982' /scratch/stefan/7916156/working/building/REAL250005073982 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073982 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073982/0 /scratch/stefan/7916156/working/building/REAL250005073982 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 89) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/89 `/scratch/stefan/7916156/working/3D/89' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC12CC1CN(C(=O)C1=CC(=O)[N-]O1)CCC2) `REAL250005073982.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073982/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073982 none CC(=O)NC12CC1CN(C(=O)C1=CC(=O)[N-]O1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 15, 15, 15, 15, 8, 1, 8, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 15, 15, 15, 15, 15, 15] 15 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: 29 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073982 none CC(=O)NC12CC1CN(C(=O)C1=CC(=O)[N-]O1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 7, 7, 15, 15, 15, 15, 15, 1, 1, 1, 2, 2, 2, 2, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1] 15 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 35, 17, 18, 19, 24, 25, 26, 27, 28, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 29]) total number of confs: 33 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073982 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073982 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073982/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073982 Building REAL250005073983 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073983' /scratch/stefan/7916156/working/building/REAL250005073983 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073983 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073983/0 /scratch/stefan/7916156/working/building/REAL250005073983 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 90) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/90 `/scratch/stefan/7916156/working/3D/90' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CO)NC12CC1CN(C(=O)C1=CC(=O)[N-]O1)CCC2) `REAL250005073983.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073983.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073983/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073983 none O=C(CO)NC12CC1CN(C(=O)C1=CC(=O)[N-]O1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 4, 7, 7, 7, 7, 7, 7, 6, 7, 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 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 37, 25, 25, 25, 25, 25, 10, 1, 10, 1, 1, 1, 1, 1, 1, 25, 25, 25, 37, 37, 111, 27, 25, 25, 25, 25, 25, 1, 25, 25, 25, 25, 25, 25] 111 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36]) total number of confs: 222 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073983 none O=C(CO)NC12CC1CN(C(=O)C1=CC(=O)[N-]O1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 4, 7, 7, 7, 7, 7, 7, 6, 7, 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 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 12, 1, 1, 1, 1, 1, 1, 1, 7, 7, 25, 25, 25, 25, 25, 1, 1, 1, 12, 12, 36, 3, 1, 1, 1, 1, 1, 25, 1, 1, 1, 1, 1, 1] 111 rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 36, 18, 19, 20, 25, 26, 27, 28, 29, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 30]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073983 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073983 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073983/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073983 Building REAL250005073984 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073984' /scratch/stefan/7916156/working/building/REAL250005073984 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073984 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073984/0 /scratch/stefan/7916156/working/building/REAL250005073984 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 91) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/91 `/scratch/stefan/7916156/working/3D/91' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N1CCCC2(NC(=O)C3=CC(=O)[N-]O3)CC2C1) `REAL250005073984.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073984.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073984/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073984 none CCC(=O)N1CCCC2(NC(=O)C3=CC(=O)[N-]O3)CC2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 5, 16, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 16, 16, 16, 16, 16, 5, 5, 5, 5, 5, 5, 5, 1, 5, 5, 5, 5, 5] 16 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: 43 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073984 none CCC(=O)N1CCCC2(NC(=O)C3=CC(=O)[N-]O3)CC2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [10, 6, 1, 6, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 1, 1, 1, 11, 11, 11, 10, 10, 1, 1, 1, 1, 1, 1, 2, 5, 1, 1, 1, 1, 1] 16 rigid atoms, others: [2, 35, 4, 5, 6, 7, 8, 9, 34, 37, 18, 19, 20, 38, 36, 26, 27, 28, 29, 30, 31] set([0, 1, 3, 33, 32, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25]) total number of confs: 51 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073984 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073984 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073984/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073984 Building REAL250005073985 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073985' /scratch/stefan/7916156/working/building/REAL250005073985 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073985 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073985/0 /scratch/stefan/7916156/working/building/REAL250005073985 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 92) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/92 `/scratch/stefan/7916156/working/3D/92' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCCC2(NC(=O)C3=CC(=O)[N-]O3)CC2C1) `REAL250005073985.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073985/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073985 none CC(=O)N1CCCC2(NC(=O)C3=CC(=O)[N-]O3)CC2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 5, 4, 4, 4, 4, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 5, 5, 5, 4, 4, 4, 4, 4, 4, 3, 1, 4, 4, 4, 4, 4] 5 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 13 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073985 none CC(=O)N1CCCC2(NC(=O)C3=CC(=O)[N-]O3)CC2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 1, 2, 4, 1, 1, 1, 1, 1] 5 rigid atoms, others: [32, 1, 34, 3, 4, 5, 6, 7, 8, 35, 33, 17, 18, 19, 23, 24, 25, 26, 27, 28, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 29, 30]) total number of confs: 16 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073985 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073985 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073985/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073985 Building REAL250005073986 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073986' /scratch/stefan/7916156/working/building/REAL250005073986 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073986 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073986/0 /scratch/stefan/7916156/working/building/REAL250005073986 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 93) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/93 `/scratch/stefan/7916156/working/3D/93' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CO)N1CCCC2(NC(=O)C3=CC(=O)[N-]O3)CC2C1) `REAL250005073986.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073986.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073986/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073986 none O=C(CO)N1CCCC2(NC(=O)C3=CC(=O)[N-]O3)CC2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [15, 6, 15, 17, 6, 6, 6, 6, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 17, 17, 51, 6, 6, 6, 6, 6, 6, 6, 1, 6, 6, 6, 6, 6] 51 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36]) total number of confs: 106 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073986 none O=C(CO)N1CCCC2(NC(=O)C3=CC(=O)[N-]O3)CC2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 12, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 1, 1, 1, 12, 12, 36, 1, 1, 1, 1, 1, 1, 2, 6, 1, 1, 1, 1, 1] 51 rigid atoms, others: [32, 1, 34, 33, 4, 5, 6, 7, 8, 9, 36, 18, 19, 20, 24, 25, 26, 27, 28, 29, 35] set([0, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 30, 31]) total number of confs: 88 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073986 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073986 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073986/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073986 Building REAL250005073987 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073987' /scratch/stefan/7916156/working/building/REAL250005073987 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073987 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073987/0 /scratch/stefan/7916156/working/building/REAL250005073987 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 94) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/94 `/scratch/stefan/7916156/working/3D/94' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(=O)N1CCCC2(NC(=O)C3=CC(=O)[N-]O3)CC2C1) `REAL250005073987.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073987/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073987 none C=CC(=O)N1CCCC2(NC(=O)C3=CC(=O)[N-]O3)CC2C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 6, 13, 6, 6, 6, 6, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 13, 13, 13, 6, 6, 6, 6, 6, 6, 6, 1, 6, 6, 6, 6, 6] 13 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36]) total number of confs: 37 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073987 none C=CC(=O)N1CCCC2(NC(=O)C3=CC(=O)[N-]O3)CC2C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [8, 6, 1, 6, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 1, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 2, 6, 1, 1, 1, 1, 1] 13 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 18, 19, 20, 24, 25, 26, 27, 28, 29, 36] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 30, 31]) total number of confs: 30 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073987 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073987 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073987/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073987 Building REAL250005073988 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073988' /scratch/stefan/7916156/working/building/REAL250005073988 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073988 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073988/0 /scratch/stefan/7916156/working/building/REAL250005073988 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 95) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/95 `/scratch/stefan/7916156/working/3D/95' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005073988.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073988/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073988 none CCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 24, 24, 24, 17, 17, 17, 16, 8, 1, 8, 1, 1, 1, 1, 1, 1, 17, 40, 40, 40, 40, 40, 24, 17, 17, 17, 17, 16, 1, 17, 17] 40 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: 154 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073988 none CCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [14, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 16, 16, 16, 16, 16, 1, 14, 14, 14, 14, 14, 3, 2, 2, 2, 1, 1, 17, 1, 1] 40 rigid atoms, others: [4, 5, 6, 7, 8, 9, 17, 27, 28, 30, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073988 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073988 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073988/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073988 Building REAL250005073989 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073989' /scratch/stefan/7916156/working/building/REAL250005073989 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073989 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073989/0 /scratch/stefan/7916156/working/building/REAL250005073989 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 96) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/96 `/scratch/stefan/7916156/working/3D/96' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005073989.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073989/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073989 none COCCC(=O)NC1(C)CN(C(=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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [85, 85, 72, 25, 25, 25, 23, 23, 23, 22, 8, 1, 8, 1, 1, 1, 1, 1, 1, 23, 85, 85, 85, 85, 85, 72, 72, 25, 23, 23, 23, 23, 22, 1, 23, 23] 85 rigid atoms, others: [33, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35]) total number of confs: 313 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073989 none COCCC(=O)NC1(C)CN(C(=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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [42, 31, 19, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 22, 22, 22, 22, 22, 1, 42, 42, 42, 31, 31, 19, 19, 3, 2, 2, 2, 1, 1, 23, 1, 1] 85 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073989 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073989 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073989/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073989 Building REAL250005073990 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073990' /scratch/stefan/7916156/working/building/REAL250005073990 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073990 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073990/0 /scratch/stefan/7916156/working/building/REAL250005073990 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 97) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/97 `/scratch/stefan/7916156/working/3D/97' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2CC2)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005073990.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073990/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073990 none CC1(NC(=O)C2CC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [23, 13, 13, 1, 13, 1, 1, 1, 23, 23, 23, 52, 52, 62, 62, 62, 62, 62, 23, 23, 23, 23, 13, 1, 1, 1, 1, 1, 23, 23, 62, 23, 23] 62 rigid atoms, others: [3, 5, 6, 7, 23, 24, 25, 26, 27] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32]) total number of confs: 180 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073990 none CC1(NC(=O)C2CC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 3, 3, 3, 23, 23, 1, 1, 1, 6, 6, 17, 17, 17, 17, 17, 1, 2, 2, 2, 3, 23, 23, 23, 23, 23, 1, 1, 17, 1, 1] 62 rigid atoms, others: [0, 1, 2, 32, 8, 9, 10, 18, 28, 29, 31] set([3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073990 none CC1(NC(=O)C2CC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 26, 26, 26, 62, 62, 17, 8, 1, 8, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 26, 62, 62, 62, 62, 62, 17, 17, 1, 17, 17] 62 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: 176 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073990 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073990 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073990/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073990 Building REAL250005073991 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073991' /scratch/stefan/7916156/working/building/REAL250005073991 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073991 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073991/0 /scratch/stefan/7916156/working/building/REAL250005073991 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 98) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/98 `/scratch/stefan/7916156/working/3D/98' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2CCC2)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005073991.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073991/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073991 none CC1(NC(=O)C2CCC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 1, 11, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [21, 12, 12, 1, 12, 1, 1, 1, 1, 21, 21, 21, 61, 61, 73, 73, 73, 73, 73, 21, 21, 21, 21, 12, 1, 1, 1, 1, 1, 1, 1, 21, 21, 73, 21, 21] 73 rigid atoms, others: [3, 5, 6, 7, 8, 24, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31, 32, 33, 34, 35]) total number of confs: 198 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073991 none CC1(NC(=O)C2CCC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 1, 11, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 3, 3, 3, 21, 21, 21, 1, 1, 1, 6, 6, 22, 22, 22, 22, 22, 1, 2, 2, 2, 3, 21, 21, 21, 21, 21, 21, 21, 1, 1, 22, 1, 1] 73 rigid atoms, others: [0, 1, 2, 35, 32, 9, 10, 11, 34, 19, 31] set([3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33]) total number of confs: 87 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.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: REAL250005073991 none CC1(NC(=O)C2CCC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 1, 11, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 34, 34, 34, 73, 73, 73, 22, 8, 1, 8, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 34, 73, 73, 73, 73, 73, 73, 73, 22, 22, 1, 22, 22] 73 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: 211 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073991 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073991 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073991/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073991 Building REAL250005073992 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073992' /scratch/stefan/7916156/working/building/REAL250005073992 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073992 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073992/0 /scratch/stefan/7916156/working/building/REAL250005073992 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 99) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/99 `/scratch/stefan/7916156/working/3D/99' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2CCCC2)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005073992.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073992/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073992 none CC1(NC(=O)C2CCCC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [19, 11, 11, 1, 11, 1, 1, 1, 1, 1, 19, 19, 19, 55, 55, 69, 69, 69, 69, 69, 19, 19, 19, 19, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 69, 19, 19] 69 rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38]) total number of confs: 180 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073992 none CC1(NC(=O)C2CCCC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 3, 3, 3, 19, 19, 19, 19, 1, 1, 1, 6, 6, 22, 22, 22, 22, 22, 1, 2, 2, 2, 3, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 23, 1, 1] 69 rigid atoms, others: [0, 1, 2, 35, 37, 38, 10, 11, 12, 34, 20] set([3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36]) total number of confs: 85 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.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: REAL250005073992 none CC1(NC(=O)C2CCCC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 23, 33, 33, 33, 69, 69, 69, 69, 22, 9, 1, 9, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 33, 69, 69, 69, 69, 69, 69, 69, 69, 69, 23, 22, 1, 23, 23] 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: 194 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073992 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073992 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073992/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073992 Building REAL250005073993 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073993' /scratch/stefan/7916156/working/building/REAL250005073993 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073993 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073993/0 /scratch/stefan/7916156/working/building/REAL250005073993 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 100) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/100 `/scratch/stefan/7916156/working/3D/100' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)CC2CC2)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005073993.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073993/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073993 none CC1(NC(=O)CC2CC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 1, 11, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 128 conformations in input total number of sets (complete confs): 128 using faster count positions algorithm for large data unique positions, atoms: [36, 22, 22, 3, 22, 1, 1, 1, 1, 36, 36, 36, 98, 98, 128, 128, 128, 128, 128, 36, 36, 36, 36, 22, 3, 3, 1, 1, 1, 1, 1, 36, 36, 128, 36, 36] 128 rigid atoms, others: [5, 6, 7, 8, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 31, 32, 33, 34, 35]) total number of confs: 344 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073993 none CC1(NC(=O)CC2CC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 1, 11, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 3, 22, 36, 36, 1, 1, 1, 6, 6, 20, 20, 20, 20, 20, 1, 2, 2, 2, 3, 22, 22, 36, 36, 36, 36, 36, 1, 1, 20, 1, 1] 128 rigid atoms, others: [0, 1, 2, 35, 32, 9, 10, 11, 34, 19, 31] set([3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073993 none CC1(NC(=O)CC2CC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 1, 11, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 128 conformations in input total number of sets (complete confs): 128 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 20, 32, 32, 32, 92, 128, 128, 20, 8, 1, 8, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 32, 92, 92, 128, 128, 128, 128, 128, 20, 20, 1, 20, 20] 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: 487 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073993 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073993 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073993/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073993 Building REAL250005073994 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073994' /scratch/stefan/7916156/working/building/REAL250005073994 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073994 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073994/0 /scratch/stefan/7916156/working/building/REAL250005073994 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 101) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/101 `/scratch/stefan/7916156/working/3D/101' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(F)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005073994.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073994/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073994 none CC(C)(F)C(=O)NC1(C)CN(C(=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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [57, 25, 57, 57, 25, 25, 18, 18, 18, 17, 8, 1, 8, 1, 1, 1, 1, 1, 1, 18, 57, 57, 57, 57, 57, 57, 25, 18, 18, 18, 17, 18, 1, 18, 18] 57 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: 203 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073994 none CC(C)(F)C(=O)NC1(C)CN(C(=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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [19, 3, 19, 19, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 17, 17, 17, 17, 17, 1, 19, 19, 19, 19, 19, 19, 3, 2, 2, 2, 1, 1, 18, 1, 1] 57 rigid atoms, others: [33, 34, 6, 7, 8, 9, 10, 11, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073994 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073994 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073994/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073994 Building REAL250005073995 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073995' /scratch/stefan/7916156/working/building/REAL250005073995 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073995 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073995/0 /scratch/stefan/7916156/working/building/REAL250005073995 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 102) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/102 `/scratch/stefan/7916156/working/3D/102' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(F)(F)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005073995.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073995.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073995/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073995 none CC(F)(F)C(=O)NC1(C)CN(C(=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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [69, 23, 69, 69, 23, 23, 15, 15, 15, 15, 7, 1, 7, 1, 1, 1, 1, 1, 1, 15, 69, 69, 69, 23, 15, 15, 15, 15, 15, 1, 15, 15] 69 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: 244 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073995 none CC(F)(F)C(=O)NC1(C)CN(C(=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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [23, 3, 23, 23, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 15, 15, 15, 15, 15, 1, 23, 23, 23, 3, 2, 2, 2, 1, 1, 15, 1, 1] 69 rigid atoms, others: [6, 7, 8, 9, 10, 11, 19, 27, 28, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 29]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073995 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073995 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073995/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073995 Building REAL250005073996 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073996' /scratch/stefan/7916156/working/building/REAL250005073996 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073996 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073996/0 /scratch/stefan/7916156/working/building/REAL250005073996 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 103) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/103 `/scratch/stefan/7916156/working/3D/103' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005073996.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073996/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073996 none COCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 27, 27, 27, 24, 24, 24, 24, 8, 1, 8, 1, 1, 1, 1, 1, 1, 24, 53, 53, 53, 53, 53, 27, 24, 24, 24, 24, 24, 1, 24, 24] 53 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: 177 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073996 none COCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [30, 17, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 24, 24, 24, 24, 24, 1, 30, 30, 30, 17, 17, 3, 2, 2, 2, 1, 1, 24, 1, 1] 53 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 18, 28, 29, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073996 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073996 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073996/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073996 Building REAL250005073997 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073997' /scratch/stefan/7916156/working/building/REAL250005073997 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073997 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073997/0 /scratch/stefan/7916156/working/building/REAL250005073997 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 104) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/104 `/scratch/stefan/7916156/working/3D/104' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005073997.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073997/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073997 none CCCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 80, 35, 35, 35, 24, 24, 24, 23, 8, 1, 8, 1, 1, 1, 1, 1, 1, 24, 90, 90, 90, 90, 90, 80, 80, 35, 24, 24, 24, 24, 23, 1, 24, 24] 90 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: 349 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073997 none CCCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [26, 19, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 23, 23, 23, 23, 23, 1, 33, 33, 33, 33, 33, 19, 19, 3, 2, 2, 2, 1, 1, 24, 1, 1] 90 rigid atoms, others: [33, 34, 5, 6, 7, 8, 9, 10, 18, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073997 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073997 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073997/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073997 Building REAL250005073998 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073998' /scratch/stefan/7916156/working/building/REAL250005073998 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073998 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073998/0 /scratch/stefan/7916156/working/building/REAL250005073998 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 105) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/105 `/scratch/stefan/7916156/working/3D/105' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC=CO2)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005073998.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073998/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073998 none CC1(NC(=O)C2=CC=CO2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [13, 7, 7, 1, 7, 1, 1, 1, 1, 1, 13, 13, 13, 28, 28, 32, 32, 32, 32, 32, 13, 13, 13, 13, 8, 1, 1, 1, 13, 13, 32, 13, 13] 32 rigid atoms, others: [3, 5, 6, 7, 8, 9, 25, 26, 27] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32]) total number of confs: 93 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073998 none CC1(NC(=O)C2=CC=CO2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 3, 3, 3, 13, 13, 13, 13, 1, 1, 1, 6, 6, 16, 16, 16, 16, 16, 1, 2, 2, 2, 3, 13, 13, 13, 1, 1, 16, 1, 1] 32 rigid atoms, others: [0, 1, 2, 32, 10, 11, 12, 20, 28, 29, 31] set([3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 30]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073998 none CC1(NC(=O)C2=CC=CO2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 23, 23, 23, 32, 32, 32, 32, 16, 9, 1, 9, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 23, 32, 32, 32, 16, 16, 1, 16, 16] 32 rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32]) total number of confs: 72 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073998 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073998 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073998/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073998 Building REAL250005073999 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005073999' /scratch/stefan/7916156/working/building/REAL250005073999 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005073999 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005073999/0 /scratch/stefan/7916156/working/building/REAL250005073999 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 106) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/106 `/scratch/stefan/7916156/working/3D/106' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005073999.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005073999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005073999/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073999 none CC(=O)NCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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, 128, 119, 34, 34, 34, 28, 28, 28, 28, 11, 1, 11, 1, 1, 1, 1, 1, 1, 28, 128, 128, 128, 128, 119, 119, 34, 28, 28, 28, 28, 28, 1, 28, 28] 128 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: 413 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005073999 none CC(=O)NCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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: [69, 69, 69, 25, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 28, 28, 28, 28, 28, 1, 69, 69, 69, 69, 25, 25, 3, 2, 2, 2, 1, 1, 28, 1, 1] 128 rigid atoms, others: [32, 34, 35, 7, 8, 9, 10, 11, 12, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33]) total number of confs: 253 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005073999 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005073999 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005073999/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005073999 Building REAL250005074000 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074000' /scratch/stefan/7916156/working/building/REAL250005074000 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074000 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074000/0 /scratch/stefan/7916156/working/building/REAL250005074000 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 107) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/107 `/scratch/stefan/7916156/working/3D/107' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074000.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074000/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074000 none CC(C)CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [51, 52, 52, 21, 21, 21, 16, 16, 16, 15, 7, 1, 7, 1, 1, 1, 1, 1, 1, 16, 52, 52, 52, 52, 52, 52, 52, 52, 52, 21, 16, 16, 16, 16, 15, 1, 16, 16] 52 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: 193 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074000 none CC(C)CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [16, 15, 19, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 15, 15, 15, 15, 15, 1, 19, 19, 19, 19, 19, 19, 19, 15, 15, 3, 2, 2, 2, 1, 1, 16, 1, 1] 52 rigid atoms, others: [33, 34, 36, 37, 6, 7, 8, 9, 10, 11, 19] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074000 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074000 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074000/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074000 Building REAL250005074001 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074001' /scratch/stefan/7916156/working/building/REAL250005074001 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074001 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074001/0 /scratch/stefan/7916156/working/building/REAL250005074001 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 108) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/108 `/scratch/stefan/7916156/working/3D/108' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC1C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074001.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074001/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074001 none CC1CC1C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 15, 2, 2, 2, 1, 1, 1, 1, 1, 1, 6, 6, 20, 20, 20, 20, 20, 1, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 2, 1, 1, 20, 1, 1] 53 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33]) total number of confs: 73 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074001 none CC1CC1C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 9, 9, 9, 15, 15, 15, 15, 44, 44, 53, 53, 53, 53, 53, 15, 2, 2, 2, 1, 1, 1, 1, 9, 15, 15, 15, 15, 15, 53, 15, 15] 53 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 25, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074001 none CC1CC1C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 26, 26, 26, 20, 20, 20, 20, 8, 1, 8, 1, 1, 1, 1, 1, 1, 20, 53, 53, 53, 53, 53, 53, 53, 26, 20, 20, 20, 20, 20, 1, 20, 20] 53 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: 142 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074001 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074001 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074001/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074001 Building REAL250005074002 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074002' /scratch/stefan/7916156/working/building/REAL250005074002 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074002 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074002/0 /scratch/stefan/7916156/working/building/REAL250005074002 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 109) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/109 `/scratch/stefan/7916156/working/3D/109' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074002.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074002/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074002 none CCOCC(=O)NC1(C)CN(C(=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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [86, 86, 80, 30, 30, 30, 25, 25, 25, 25, 9, 1, 9, 1, 1, 1, 1, 1, 1, 25, 86, 86, 86, 86, 86, 80, 80, 30, 25, 25, 25, 25, 25, 1, 25, 25] 86 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: 268 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074002 none CCOCC(=O)NC1(C)CN(C(=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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [49, 45, 19, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 25, 25, 25, 25, 25, 1, 49, 49, 49, 49, 49, 19, 19, 3, 2, 2, 2, 1, 1, 25, 1, 1] 86 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33]) total number of confs: 166 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074002 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074002 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074002/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074002 Building REAL250005074003 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074003' /scratch/stefan/7916156/working/building/REAL250005074003 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074003 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074003/0 /scratch/stefan/7916156/working/building/REAL250005074003 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 110) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/110 `/scratch/stefan/7916156/working/3D/110' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)=CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074003.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074003/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074003 none CC(C)=CC(=O)NC1(C)CN(C(=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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 22, 22, 22, 18, 18, 18, 18, 9, 1, 9, 1, 1, 1, 1, 1, 1, 18, 35, 35, 35, 35, 35, 35, 35, 22, 18, 18, 18, 18, 18, 1, 18, 18] 35 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: 93 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074003 none CC(C)=CC(=O)NC1(C)CN(C(=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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 18, 18, 18, 18, 18, 1, 11, 11, 11, 11, 11, 11, 11, 3, 2, 2, 2, 1, 1, 18, 1, 1] 35 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074003 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074003 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074003/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074003 Building REAL250005074004 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074004' /scratch/stefan/7916156/working/building/REAL250005074004 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074004 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074004/0 /scratch/stefan/7916156/working/building/REAL250005074004 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 111) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/111 `/scratch/stefan/7916156/working/3D/111' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2CCCO2)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074004.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074004/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074004 none CC1(NC(=O)C2CCCO2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [20, 11, 11, 1, 11, 1, 1, 1, 1, 1, 20, 20, 20, 54, 54, 64, 64, 64, 64, 64, 20, 20, 20, 20, 11, 1, 1, 1, 1, 1, 1, 1, 20, 20, 64, 20, 20] 64 rigid atoms, others: [3, 5, 6, 7, 8, 9, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36]) total number of confs: 179 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074004 none CC1(NC(=O)C2CCCO2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 3, 3, 3, 20, 20, 20, 20, 1, 1, 1, 6, 6, 23, 23, 23, 23, 23, 1, 2, 2, 2, 3, 20, 20, 20, 20, 20, 20, 20, 1, 1, 23, 1, 1] 64 rigid atoms, others: [0, 1, 2, 35, 36, 33, 32, 10, 11, 12, 20] set([3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074004 none CC1(NC(=O)C2CCCO2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 23, 32, 32, 32, 64, 64, 64, 64, 23, 8, 1, 8, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 32, 64, 64, 64, 64, 64, 64, 64, 23, 23, 1, 23, 23] 64 rigid atoms, others: [34, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36]) total number of confs: 169 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074004 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074004 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074004/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074004 Building REAL250005074005 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074005' /scratch/stefan/7916156/working/building/REAL250005074005 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074005 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074005/0 /scratch/stefan/7916156/working/building/REAL250005074005 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 112) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/112 `/scratch/stefan/7916156/working/3D/112' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074005.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074005.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074005/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074005 none CSCC(=O)NC1(C)CN(C(=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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [94, 82, 29, 29, 29, 23, 23, 23, 23, 9, 1, 9, 1, 1, 1, 1, 1, 1, 23, 94, 94, 94, 82, 82, 29, 23, 23, 23, 23, 23, 1, 23, 23] 94 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32]) total number of confs: 303 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074005 none CSCC(=O)NC1(C)CN(C(=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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [49, 21, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 23, 23, 23, 23, 23, 1, 49, 49, 49, 21, 21, 3, 2, 2, 2, 1, 1, 23, 1, 1] 94 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 18, 28, 29, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074005 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074005 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074005/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074005 Building REAL250005074006 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074006' /scratch/stefan/7916156/working/building/REAL250005074006 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074006 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074006/0 /scratch/stefan/7916156/working/building/REAL250005074006 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 113) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/113 `/scratch/stefan/7916156/working/3D/113' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSCCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074006.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074006/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074006 none CSCCC(=O)NC1(C)CN(C(=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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 136 conformations in input total number of sets (complete confs): 136 using faster count positions algorithm for large data unique positions, atoms: [136, 93, 85, 28, 28, 28, 22, 22, 22, 21, 9, 1, 9, 1, 1, 1, 1, 1, 1, 22, 136, 136, 136, 93, 93, 85, 85, 28, 22, 22, 22, 22, 21, 1, 22, 22] 136 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: 408 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074006 none CSCCC(=O)NC1(C)CN(C(=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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 136 conformations in input total number of sets (complete confs): 136 using faster count positions algorithm for large data unique positions, atoms: [74, 30, 18, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 21, 21, 21, 21, 21, 1, 74, 74, 74, 30, 30, 18, 18, 3, 2, 2, 2, 1, 1, 22, 1, 1] 136 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33]) total number of confs: 231 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074006 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074006 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074006/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074006 Building REAL250005074007 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074007' /scratch/stefan/7916156/working/building/REAL250005074007 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074007 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074007/0 /scratch/stefan/7916156/working/building/REAL250005074007 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 114) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/114 `/scratch/stefan/7916156/working/3D/114' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074007.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074007.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074007/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074007 none CC(C)CCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [131, 128, 132, 122, 38, 38, 38, 26, 26, 26, 25, 10, 1, 10, 1, 1, 1, 1, 1, 1, 26, 132, 132, 131, 132, 132, 132, 132, 128, 128, 122, 122, 38, 26, 26, 26, 26, 25, 1, 26, 26] 132 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: 500 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074007 none CC(C)CCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [35, 32, 41, 19, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 25, 25, 25, 25, 25, 1, 41, 41, 35, 41, 41, 41, 41, 32, 32, 19, 19, 3, 2, 2, 2, 1, 1, 26, 1, 1] 132 rigid atoms, others: [36, 37, 7, 8, 9, 10, 11, 12, 40, 20, 39] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38]) total number of confs: 259 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074007 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074007 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074007/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074007 Building REAL250005074008 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074008' /scratch/stefan/7916156/working/building/REAL250005074008 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074008 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074008/0 /scratch/stefan/7916156/working/building/REAL250005074008 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 115) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/115 `/scratch/stefan/7916156/working/3D/115' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC=CN2)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074008.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074008/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074008 none CC1(NC(=O)C2=CC=CN2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [15, 9, 9, 1, 9, 1, 1, 1, 1, 1, 15, 15, 15, 30, 30, 35, 35, 35, 35, 35, 15, 15, 15, 15, 9, 1, 1, 1, 1, 15, 15, 35, 15, 15] 35 rigid atoms, others: [3, 5, 6, 7, 8, 9, 25, 26, 27, 28] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33]) total number of confs: 99 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074008 none CC1(NC(=O)C2=CC=CN2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 3, 3, 3, 15, 15, 15, 15, 1, 1, 1, 6, 6, 11, 11, 11, 11, 11, 1, 2, 2, 2, 3, 15, 15, 15, 15, 1, 1, 12, 1, 1] 35 rigid atoms, others: [0, 1, 2, 33, 32, 10, 11, 12, 20, 29, 30] set([3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 31]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074008 none CC1(NC(=O)C2=CC=CN2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 20, 20, 20, 35, 35, 35, 35, 11, 4, 1, 4, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 20, 35, 35, 35, 35, 12, 11, 1, 12, 12] 35 rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33]) total number of confs: 81 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074008 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074008 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074008/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074008 Building REAL250005074009 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074009' /scratch/stefan/7916156/working/building/REAL250005074009 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074009 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074009/0 /scratch/stefan/7916156/working/building/REAL250005074009 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 116) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/116 `/scratch/stefan/7916156/working/3D/116' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=COC=C2)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074009.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074009/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074009 none CC1(NC(=O)C2=COC=C2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 12, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 9, 9, 9, 30, 30, 38, 38, 38, 38, 38, 9, 9, 9, 9, 5, 1, 1, 1, 9, 9, 38, 9, 9] 38 rigid atoms, others: [3, 5, 6, 7, 8, 9, 25, 26, 27] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32]) total number of confs: 101 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074009 none CC1(NC(=O)C2=COC=C2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 12, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 1, 1, 1, 6, 6, 13, 13, 13, 13, 13, 1, 2, 2, 2, 3, 9, 9, 9, 1, 1, 13, 1, 1] 38 rigid atoms, others: [0, 1, 2, 32, 10, 11, 12, 20, 28, 29, 31] set([3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 30]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074009 none CC1(NC(=O)C2=COC=C2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 12, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 21, 21, 21, 38, 38, 38, 38, 13, 6, 1, 6, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 21, 38, 38, 38, 13, 13, 1, 13, 13] 38 rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32]) total number of confs: 89 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074009 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074009 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074009/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074009 Building REAL250005074010 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074010' /scratch/stefan/7916156/working/building/REAL250005074010 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074010 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074010/0 /scratch/stefan/7916156/working/building/REAL250005074010 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 117) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/117 `/scratch/stefan/7916156/working/3D/117' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074010.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074010.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074010/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074010 none CCCCCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [194, 189, 138, 109, 25, 25, 25, 20, 20, 20, 19, 6, 1, 6, 1, 1, 1, 1, 1, 1, 20, 196, 201, 201, 201, 201, 189, 187, 149, 149, 109, 109, 25, 20, 20, 20, 20, 19, 1, 20, 20] 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: 941 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074010 none CCCCCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [86, 65, 32, 19, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 19, 19, 19, 19, 19, 1, 98, 109, 109, 109, 109, 67, 66, 39, 39, 19, 19, 3, 2, 2, 2, 1, 1, 20, 1, 1] 201 rigid atoms, others: [36, 37, 7, 8, 9, 10, 11, 12, 40, 20, 39] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38]) total number of confs: 684 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074010 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074010 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074010/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074010 Building REAL250005074011 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074011' /scratch/stefan/7916156/working/building/REAL250005074011 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074011 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074011/0 /scratch/stefan/7916156/working/building/REAL250005074011 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 118) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/118 `/scratch/stefan/7916156/working/3D/118' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074011.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074011/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074011 none CC(C)(C)CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [33, 32, 33, 33, 21, 21, 21, 19, 19, 19, 19, 9, 1, 9, 1, 1, 1, 1, 1, 1, 19, 33, 33, 33, 33, 33, 33, 33, 33, 33, 32, 32, 21, 19, 19, 19, 19, 19, 1, 19, 19] 33 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: 103 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074011 none CC(C)(C)CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [12, 9, 12, 12, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 19, 19, 19, 19, 19, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 9, 9, 3, 2, 2, 2, 1, 1, 19, 1, 1] 33 rigid atoms, others: [36, 37, 7, 8, 9, 10, 11, 12, 40, 20, 39] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074011 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074011 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074011/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074011 Building REAL250005074012 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074012' /scratch/stefan/7916156/working/building/REAL250005074012 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074012 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074012/0 /scratch/stefan/7916156/working/building/REAL250005074012 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 119) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/119 `/scratch/stefan/7916156/working/3D/119' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074012.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074012/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074012 none CCCCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [157, 144, 131, 36, 36, 36, 25, 25, 25, 24, 10, 1, 10, 1, 1, 1, 1, 1, 1, 25, 157, 160, 160, 160, 160, 145, 145, 131, 131, 36, 25, 25, 25, 25, 24, 1, 25, 25] 160 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: 653 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074012 none CCCCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [66, 31, 19, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 24, 24, 24, 24, 24, 1, 66, 71, 71, 65, 66, 38, 38, 19, 19, 3, 2, 2, 2, 1, 1, 25, 1, 1] 160 rigid atoms, others: [33, 34, 36, 37, 6, 7, 8, 9, 10, 11, 19] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35]) total number of confs: 399 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074012 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074012 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074012/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074012 Building REAL250005074013 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074013' /scratch/stefan/7916156/working/building/REAL250005074013 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074013 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074013/0 /scratch/stefan/7916156/working/building/REAL250005074013 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 120) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/120 `/scratch/stefan/7916156/working/3D/120' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074013.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074013.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074013/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074013 none CC(C)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [43, 26, 43, 26, 26, 19, 19, 19, 18, 7, 1, 7, 1, 1, 1, 1, 1, 1, 19, 43, 43, 43, 43, 43, 43, 43, 26, 19, 19, 19, 19, 18, 1, 19, 19] 43 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: 147 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074013 none CC(C)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [12, 3, 12, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 18, 18, 18, 18, 18, 1, 12, 12, 12, 12, 12, 12, 12, 3, 2, 2, 2, 1, 1, 19, 1, 1] 43 rigid atoms, others: [33, 34, 5, 6, 7, 8, 9, 10, 18, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074013 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074013 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074013/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074013 Building REAL250005074014 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074014' /scratch/stefan/7916156/working/building/REAL250005074014 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074014 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074014/0 /scratch/stefan/7916156/working/building/REAL250005074014 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 121) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/121 `/scratch/stefan/7916156/working/3D/121' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074014.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074014.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074014/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074014 none CCC(C)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [79, 69, 28, 69, 28, 28, 22, 22, 22, 21, 7, 1, 7, 1, 1, 1, 1, 1, 1, 22, 79, 79, 79, 79, 79, 69, 69, 69, 69, 28, 22, 22, 22, 22, 21, 1, 22, 22] 79 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: 299 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074014 none CCC(C)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [29, 21, 3, 21, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 21, 21, 21, 21, 21, 1, 32, 32, 32, 32, 32, 21, 21, 21, 21, 3, 2, 2, 2, 1, 1, 22, 1, 1] 79 rigid atoms, others: [33, 34, 36, 37, 6, 7, 8, 9, 10, 11, 19] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074014 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074014 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074014/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074014 Building REAL250005074015 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074015' /scratch/stefan/7916156/working/building/REAL250005074015 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074015 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074015/0 /scratch/stefan/7916156/working/building/REAL250005074015 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 122) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/122 `/scratch/stefan/7916156/working/3D/122' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074015.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074015/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074015 none CCC(CC)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [40, 33, 16, 33, 39, 16, 16, 14, 14, 14, 14, 7, 1, 7, 1, 1, 1, 1, 1, 1, 14, 40, 40, 40, 40, 40, 33, 39, 39, 39, 39, 39, 16, 14, 14, 14, 14, 13, 1, 14, 14] 41 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: 181 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074015 none CCC(CC)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [16, 11, 3, 11, 14, 3, 3, 1, 1, 1, 1, 1, 1, 5, 5, 13, 13, 13, 13, 14, 1, 16, 16, 16, 16, 16, 11, 14, 14, 14, 14, 14, 3, 2, 2, 2, 1, 1, 14, 1, 1] 41 rigid atoms, others: [36, 37, 7, 8, 9, 10, 11, 12, 40, 20, 39] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074015 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074015 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074015/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074015 Building REAL250005074016 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074016' /scratch/stefan/7916156/working/building/REAL250005074016 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074016 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074016/0 /scratch/stefan/7916156/working/building/REAL250005074016 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 123) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/123 `/scratch/stefan/7916156/working/3D/123' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC=NN2)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074016.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074016/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074016 none CC1(NC(=O)C2=CC=NN2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 8, 8, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [13, 7, 7, 1, 7, 1, 1, 1, 1, 1, 13, 13, 13, 27, 27, 30, 30, 30, 30, 30, 13, 13, 13, 13, 7, 1, 1, 1, 13, 13, 30, 13, 13] 30 rigid atoms, others: [3, 5, 6, 7, 8, 9, 25, 26, 27] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32]) total number of confs: 87 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074016 none CC1(NC(=O)C2=CC=NN2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 8, 8, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 3, 13, 13, 13, 13, 1, 1, 1, 7, 7, 12, 12, 12, 12, 12, 1, 2, 2, 2, 3, 13, 13, 13, 1, 1, 12, 1, 1] 30 rigid atoms, others: [0, 1, 2, 32, 10, 11, 12, 20, 28, 29, 31] set([3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 30]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074016 none CC1(NC(=O)C2=CC=NN2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 8, 8, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 18, 18, 18, 30, 30, 30, 30, 12, 5, 1, 5, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 18, 30, 30, 30, 12, 12, 1, 12, 12] 30 rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32]) total number of confs: 64 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074016 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074016 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074016/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074016 Building REAL250005074017 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074017' /scratch/stefan/7916156/working/building/REAL250005074017 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074017 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074017/0 /scratch/stefan/7916156/working/building/REAL250005074017 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 124) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/124 `/scratch/stefan/7916156/working/3D/124' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSC(C)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074017.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074017/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074017 none CSC(C)C(=O)NC1(C)CN(C(=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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [93, 78, 29, 78, 29, 29, 24, 24, 24, 24, 11, 1, 11, 1, 1, 1, 1, 1, 1, 24, 93, 93, 93, 78, 78, 78, 78, 29, 24, 24, 24, 24, 24, 1, 24, 24] 93 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: 293 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074017 none CSC(C)C(=O)NC1(C)CN(C(=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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [47, 20, 3, 20, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 24, 24, 24, 24, 24, 1, 47, 47, 47, 20, 20, 20, 20, 3, 2, 2, 2, 1, 1, 24, 1, 1] 93 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074017 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074017 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074017/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074017 Building REAL250005074018 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074018' /scratch/stefan/7916156/working/building/REAL250005074018 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074018 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074018/0 /scratch/stefan/7916156/working/building/REAL250005074018 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 125) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/125 `/scratch/stefan/7916156/working/3D/125' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(C)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074018.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074018/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074018 none CCOC(C)C(=O)NC1(C)CN(C(=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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 61, 29, 61, 29, 29, 24, 24, 24, 24, 10, 1, 10, 1, 1, 1, 1, 1, 1, 24, 63, 63, 63, 63, 63, 61, 61, 61, 61, 29, 24, 24, 24, 24, 24, 1, 24, 24] 63 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: 206 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074018 none CCOC(C)C(=O)NC1(C)CN(C(=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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [33, 33, 19, 3, 19, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 24, 24, 24, 24, 24, 1, 33, 33, 33, 33, 33, 19, 19, 19, 19, 3, 2, 2, 2, 1, 1, 24, 1, 1] 63 rigid atoms, others: [34, 35, 37, 38, 7, 8, 9, 10, 11, 12, 20] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074018 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074018 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074018/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074018 Building REAL250005074019 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074019' /scratch/stefan/7916156/working/building/REAL250005074019 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074019 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074019/0 /scratch/stefan/7916156/working/building/REAL250005074019 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 126) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/126 `/scratch/stefan/7916156/working/3D/126' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CNN=C2)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074019.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074019/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074019 none CC1(NC(=O)C2=CNN=C2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 8, 8, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 3, 1, 3, 1, 1, 1, 1, 1, 5, 5, 5, 16, 16, 21, 21, 21, 21, 21, 5, 5, 5, 5, 3, 1, 1, 1, 5, 5, 21, 5, 5] 21 rigid atoms, others: [3, 5, 6, 7, 8, 9, 25, 26, 27] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32]) total number of confs: 55 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074019 none CC1(NC(=O)C2=CNN=C2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 8, 8, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 1, 1, 1, 6, 6, 15, 15, 15, 15, 15, 1, 2, 2, 2, 3, 5, 5, 5, 1, 1, 15, 1, 1] 21 rigid atoms, others: [0, 1, 2, 32, 10, 11, 12, 20, 28, 29, 31] set([3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 30]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074019 none CC1(NC(=O)C2=CNN=C2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 8, 8, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 21, 21, 21, 21, 21, 21, 21, 15, 8, 1, 8, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 21, 21, 21, 21, 15, 15, 1, 15, 15] 21 rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32]) total number of confs: 51 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074019 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074019 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074019/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074019 Building REAL250005074020 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074020' /scratch/stefan/7916156/working/building/REAL250005074020 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074020 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074020/0 /scratch/stefan/7916156/working/building/REAL250005074020 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 127) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/127 `/scratch/stefan/7916156/working/3D/127' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074020.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074020/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074020 none COCCCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [129, 129, 80, 66, 17, 17, 17, 14, 14, 14, 13, 4, 1, 4, 1, 1, 1, 1, 1, 1, 14, 129, 129, 129, 122, 120, 94, 94, 66, 66, 17, 14, 14, 14, 14, 13, 1, 14, 14] 129 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: 592 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074020 none COCCCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [89, 71, 30, 19, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 13, 13, 13, 13, 13, 1, 89, 89, 89, 63, 66, 39, 39, 19, 19, 3, 2, 2, 2, 1, 1, 14, 1, 1] 129 rigid atoms, others: [34, 35, 37, 38, 7, 8, 9, 10, 11, 12, 20] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36]) total number of confs: 402 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074020 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074020 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074020/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074020 Building REAL250005074021 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074021' /scratch/stefan/7916156/working/building/REAL250005074021 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074021 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074021/0 /scratch/stefan/7916156/working/building/REAL250005074021 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 128) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/128 `/scratch/stefan/7916156/working/3D/128' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=NOC=C2)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074021.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074021/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074021 none CC1(NC(=O)C2=NOC=C2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 8, 12, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [13, 8, 8, 1, 8, 1, 1, 1, 1, 1, 13, 13, 13, 26, 26, 31, 31, 31, 31, 31, 13, 13, 13, 13, 8, 1, 1, 13, 13, 31, 13, 13] 31 rigid atoms, others: [3, 5, 6, 7, 8, 9, 25, 26] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31]) total number of confs: 85 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074021 none CC1(NC(=O)C2=NOC=C2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 8, 12, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 3, 3, 3, 13, 13, 13, 13, 1, 1, 1, 6, 6, 14, 14, 14, 14, 14, 1, 2, 2, 2, 3, 13, 13, 1, 1, 14, 1, 1] 31 rigid atoms, others: [0, 1, 2, 10, 11, 12, 20, 27, 28, 30, 31] set([3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 29]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074021 none CC1(NC(=O)C2=NOC=C2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 8, 12, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 22, 22, 22, 31, 31, 31, 31, 14, 7, 1, 7, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 22, 31, 31, 14, 14, 1, 14, 14] 31 rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31]) total number of confs: 73 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074021 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074021 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074021/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074021 Building REAL250005074022 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074022' /scratch/stefan/7916156/working/building/REAL250005074022 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074022 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074022/0 /scratch/stefan/7916156/working/building/REAL250005074022 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 129) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/129 `/scratch/stefan/7916156/working/3D/129' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC=C(C)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074022.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074022/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074022 none CCC=C(C)C(=O)NC1(C)CN(C(=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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [93, 90, 90, 18, 90, 18, 18, 12, 12, 12, 12, 5, 1, 5, 1, 1, 1, 1, 1, 1, 12, 93, 93, 93, 93, 93, 90, 90, 90, 90, 18, 12, 12, 12, 12, 12, 1, 12, 12] 93 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: 237 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074022 none CCC=C(C)C(=O)NC1(C)CN(C(=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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [30, 18, 18, 3, 18, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 12, 12, 12, 12, 12, 1, 30, 30, 30, 30, 30, 18, 18, 18, 18, 3, 2, 2, 2, 1, 1, 12, 1, 1] 93 rigid atoms, others: [34, 35, 37, 38, 7, 8, 9, 10, 11, 12, 20] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36]) total number of confs: 136 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074022 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074022 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074022/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074022 Building REAL250005074023 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074023' /scratch/stefan/7916156/working/building/REAL250005074023 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074023 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074023/0 /scratch/stefan/7916156/working/building/REAL250005074023 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 130) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/130 `/scratch/stefan/7916156/working/3D/130' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074023.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074023.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074023/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074023 none COC(C)C(=O)NC1(C)CN(C(=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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [40, 39, 22, 39, 22, 22, 19, 19, 19, 19, 10, 1, 10, 1, 1, 1, 1, 1, 1, 19, 40, 40, 40, 39, 39, 39, 39, 22, 19, 19, 19, 19, 19, 1, 19, 19] 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: 127 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074023 none COC(C)C(=O)NC1(C)CN(C(=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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [21, 17, 3, 17, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 19, 19, 19, 19, 19, 1, 21, 21, 21, 17, 17, 17, 17, 3, 2, 2, 2, 1, 1, 19, 1, 1] 40 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074023 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074023 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074023/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074023 Building REAL250005074024 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074024' /scratch/stefan/7916156/working/building/REAL250005074024 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074024 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074024/0 /scratch/stefan/7916156/working/building/REAL250005074024 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 131) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/131 `/scratch/stefan/7916156/working/3D/131' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)OCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074024.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074024/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074024 none CC(C)OCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [125, 121, 125, 100, 29, 29, 29, 24, 24, 24, 24, 10, 1, 10, 1, 1, 1, 1, 1, 1, 24, 125, 125, 125, 125, 125, 125, 125, 100, 100, 29, 24, 24, 24, 24, 24, 1, 24, 24] 125 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.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074024 none CC(C)OCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [66, 52, 66, 20, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 24, 24, 24, 24, 24, 1, 66, 66, 66, 66, 66, 66, 66, 20, 20, 3, 2, 2, 2, 1, 1, 24, 1, 1] 125 rigid atoms, others: [34, 35, 37, 38, 7, 8, 9, 10, 11, 12, 20] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074024 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074024 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074024/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074024 Building REAL250005074025 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074025' /scratch/stefan/7916156/working/building/REAL250005074025 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074025 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074025/0 /scratch/stefan/7916156/working/building/REAL250005074025 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 132) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/132 `/scratch/stefan/7916156/working/3D/132' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074025.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074025.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074025/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074025 none CCCOCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 134, 83, 22, 22, 22, 18, 18, 18, 18, 6, 1, 6, 1, 1, 1, 1, 1, 1, 18, 201, 201, 201, 201, 201, 175, 175, 83, 83, 22, 18, 18, 18, 18, 18, 1, 18, 18] 201 rigid atoms, others: [36, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 732 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074025 none CCCOCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [155, 113, 57, 20, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 18, 18, 18, 18, 18, 1, 155, 155, 155, 155, 155, 113, 113, 20, 20, 3, 2, 2, 2, 1, 1, 18, 1, 1] 201 rigid atoms, others: [34, 35, 37, 38, 7, 8, 9, 10, 11, 12, 20] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36]) total number of confs: 649 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074025 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074025 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074025/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074025 Building REAL250005074026 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074026' /scratch/stefan/7916156/working/building/REAL250005074026 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074026 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074026/0 /scratch/stefan/7916156/working/building/REAL250005074026 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 133) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/133 `/scratch/stefan/7916156/working/3D/133' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2CCOC2)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074026.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074026/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074026 none CC1(NC(=O)C2CCOC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [17, 9, 9, 1, 9, 1, 1, 1, 1, 1, 17, 17, 17, 52, 52, 62, 62, 62, 62, 62, 17, 17, 17, 17, 9, 1, 1, 1, 1, 1, 1, 1, 17, 17, 62, 17, 17] 62 rigid atoms, others: [3, 5, 6, 7, 8, 9, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36]) total number of confs: 171 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074026 none CC1(NC(=O)C2CCOC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 3, 3, 3, 17, 17, 17, 17, 1, 1, 1, 6, 6, 18, 18, 18, 18, 18, 1, 2, 2, 2, 3, 17, 17, 17, 17, 17, 17, 17, 1, 1, 19, 1, 1] 62 rigid atoms, others: [0, 1, 2, 35, 36, 33, 32, 10, 11, 12, 20] set([3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34]) 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.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: REAL250005074026 none CC1(NC(=O)C2CCOC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [19, 19, 19, 29, 29, 29, 62, 62, 62, 62, 18, 7, 1, 7, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 29, 62, 62, 62, 62, 62, 62, 62, 19, 18, 1, 19, 19] 62 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: 177 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074026 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074026 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074026/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074026 Building REAL250005074027 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074027' /scratch/stefan/7916156/working/building/REAL250005074027 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074027 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074027/0 /scratch/stefan/7916156/working/building/REAL250005074027 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 134) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/134 `/scratch/stefan/7916156/working/3D/134' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(OC)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074027.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074027/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074027 none CCC(OC)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [64, 60, 24, 60, 64, 24, 24, 22, 22, 22, 22, 10, 1, 10, 1, 1, 1, 1, 1, 1, 22, 69, 69, 69, 69, 69, 60, 64, 64, 64, 24, 22, 22, 22, 22, 22, 1, 22, 22] 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: 293 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074027 none CCC(OC)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [20, 16, 3, 16, 23, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 22, 22, 22, 22, 22, 1, 25, 25, 25, 25, 25, 16, 23, 23, 23, 3, 2, 2, 2, 1, 1, 22, 1, 1] 69 rigid atoms, others: [34, 35, 37, 38, 7, 8, 9, 10, 11, 12, 20] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074027 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074027 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074027/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074027 Building REAL250005074028 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074028' /scratch/stefan/7916156/working/building/REAL250005074028 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074028 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074028/0 /scratch/stefan/7916156/working/building/REAL250005074028 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 135) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/135 `/scratch/stefan/7916156/working/3D/135' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074028.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074028/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074028 none COC(C)CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 126 conformations in input total number of sets (complete confs): 126 using faster count positions algorithm for large data unique positions, atoms: [126, 126, 105, 124, 34, 34, 34, 26, 26, 26, 26, 12, 1, 12, 1, 1, 1, 1, 1, 1, 26, 126, 126, 126, 126, 126, 126, 126, 105, 105, 34, 26, 26, 26, 26, 26, 1, 26, 26] 126 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: 478 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074028 none COC(C)CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 126 conformations in input total number of sets (complete confs): 126 using faster count positions algorithm for large data unique positions, atoms: [55, 47, 22, 45, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 26, 26, 26, 26, 26, 1, 55, 55, 55, 47, 47, 47, 47, 22, 22, 3, 2, 2, 2, 1, 1, 26, 1, 1] 126 rigid atoms, others: [34, 35, 37, 38, 7, 8, 9, 10, 11, 12, 20] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36]) total number of confs: 262 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074028 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074028 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074028/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074028 Building REAL250005074029 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074029' /scratch/stefan/7916156/working/building/REAL250005074029 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074029 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074029/0 /scratch/stefan/7916156/working/building/REAL250005074029 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 136) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/136 `/scratch/stefan/7916156/working/3D/136' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074029.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074029/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074029 none C=CCCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 133 conformations in input total number of sets (complete confs): 133 using faster count positions algorithm for large data unique positions, atoms: [133, 133, 104, 31, 31, 31, 25, 25, 25, 24, 9, 1, 9, 1, 1, 1, 1, 1, 1, 25, 133, 133, 133, 133, 133, 104, 104, 31, 25, 25, 25, 25, 24, 1, 25, 25] 133 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: 505 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074029 none C=CCCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 133 conformations in input total number of sets (complete confs): 133 using faster count positions algorithm for large data unique positions, atoms: [70, 36, 18, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 24, 24, 24, 24, 24, 1, 70, 70, 70, 36, 36, 18, 18, 3, 2, 2, 2, 1, 1, 25, 1, 1] 133 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33]) total number of confs: 306 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074029 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074029 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074029/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074029 Building REAL250005074030 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074030' /scratch/stefan/7916156/working/building/REAL250005074030 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074030 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074030/0 /scratch/stefan/7916156/working/building/REAL250005074030 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 137) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/137 `/scratch/stefan/7916156/working/3D/137' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074030.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074030/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074030 none CCOCCC(=O)NC1(C)CN(C(=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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 123, 115, 84, 25, 25, 25, 22, 22, 22, 21, 8, 1, 8, 1, 1, 1, 1, 1, 1, 22, 128, 128, 128, 128, 128, 115, 115, 84, 84, 25, 22, 22, 22, 22, 21, 1, 22, 22] 128 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: 500 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074030 none CCOCCC(=O)NC1(C)CN(C(=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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [83, 70, 38, 19, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 21, 21, 21, 21, 21, 1, 83, 83, 83, 83, 83, 38, 38, 19, 19, 3, 2, 2, 2, 1, 1, 22, 1, 1] 128 rigid atoms, others: [34, 35, 37, 38, 7, 8, 9, 10, 11, 12, 20] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36]) total number of confs: 327 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074030 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074030 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074030/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074030 Building REAL250005074031 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074031' /scratch/stefan/7916156/working/building/REAL250005074031 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074031 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074031/0 /scratch/stefan/7916156/working/building/REAL250005074031 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 138) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/138 `/scratch/stefan/7916156/working/3D/138' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(C)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074031.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074031.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074031/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074031 none COCC(C)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [83, 83, 65, 26, 65, 26, 26, 22, 22, 22, 21, 9, 1, 9, 1, 1, 1, 1, 1, 1, 22, 83, 83, 83, 83, 83, 65, 65, 65, 65, 26, 22, 22, 22, 22, 21, 1, 22, 22] 83 rigid atoms, others: [36, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 307 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074031 none COCC(C)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [56, 46, 19, 3, 19, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 21, 21, 21, 21, 21, 1, 56, 56, 56, 46, 46, 19, 19, 19, 19, 3, 2, 2, 2, 1, 1, 22, 1, 1] 83 rigid atoms, others: [34, 35, 37, 38, 7, 8, 9, 10, 11, 12, 20] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36]) total number of confs: 238 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074031 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074031 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074031/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074031 Building REAL250005074032 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074032' /scratch/stefan/7916156/working/building/REAL250005074032 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074032 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074032/0 /scratch/stefan/7916156/working/building/REAL250005074032 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 139) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/139 `/scratch/stefan/7916156/working/3D/139' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCOCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074032.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074032/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074032 none C=CCOCC(=O)NC1(C)CN(C(=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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 142, 82, 21, 21, 21, 17, 17, 17, 17, 6, 1, 6, 1, 1, 1, 1, 1, 1, 17, 201, 201, 201, 201, 201, 82, 82, 21, 17, 17, 17, 17, 17, 1, 17, 17] 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: 680 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074032 none C=CCOCC(=O)NC1(C)CN(C(=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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 112, 49, 17, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 17, 17, 17, 17, 17, 1, 154, 154, 154, 112, 112, 17, 17, 3, 2, 2, 2, 1, 1, 17, 1, 1] 201 rigid atoms, others: [32, 33, 35, 36, 7, 8, 9, 10, 11, 12, 20] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34]) total number of confs: 546 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074032 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074032 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074032/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074032 Building REAL250005074033 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074033' /scratch/stefan/7916156/working/building/REAL250005074033 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074033 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074033/0 /scratch/stefan/7916156/working/building/REAL250005074033 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 140) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/140 `/scratch/stefan/7916156/working/3D/140' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=COC=N2)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074033.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074033.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074033/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074033 none CC1(NC(=O)C2=COC=N2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'N.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 12, 1, 8, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 6, 1, 6, 1, 1, 1, 1, 1, 11, 11, 11, 23, 23, 27, 27, 27, 27, 27, 11, 11, 11, 11, 6, 1, 1, 11, 11, 27, 11, 11] 27 rigid atoms, others: [3, 5, 6, 7, 8, 9, 25, 26] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31]) total number of confs: 75 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074033 none CC1(NC(=O)C2=COC=N2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'N.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 12, 1, 8, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 3, 3, 3, 11, 11, 11, 11, 1, 1, 1, 6, 6, 15, 15, 15, 15, 15, 1, 2, 2, 2, 3, 11, 11, 1, 1, 16, 1, 1] 27 rigid atoms, others: [0, 1, 2, 10, 11, 12, 20, 27, 28, 30, 31] set([3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 29]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074033 none CC1(NC(=O)C2=COC=N2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'N.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 12, 1, 8, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 21, 21, 21, 27, 27, 27, 27, 15, 8, 1, 8, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 21, 27, 27, 15, 16, 1, 16, 16] 27 rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31]) total number of confs: 62 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074033 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074033 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074033/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074033 Building REAL250005074034 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074034' /scratch/stefan/7916156/working/building/REAL250005074034 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074034 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074034/0 /scratch/stefan/7916156/working/building/REAL250005074034 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 141) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/141 `/scratch/stefan/7916156/working/3D/141' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(C)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074034.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074034.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074034/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074034 none CCCC(C)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 103, 92, 28, 92, 28, 28, 22, 22, 22, 21, 8, 1, 8, 1, 1, 1, 1, 1, 1, 22, 105, 105, 105, 105, 105, 103, 103, 92, 92, 92, 92, 28, 22, 22, 22, 22, 21, 1, 22, 22] 105 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: 395 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074034 none CCCC(C)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [43, 37, 20, 3, 20, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 21, 21, 21, 21, 21, 1, 43, 43, 43, 42, 43, 38, 38, 20, 20, 20, 20, 3, 2, 2, 2, 1, 1, 22, 1, 1] 105 rigid atoms, others: [36, 37, 7, 8, 9, 10, 11, 12, 40, 20, 39] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38]) total number of confs: 227 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074034 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074034 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074034/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074034 Building REAL250005074035 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074035' /scratch/stefan/7916156/working/building/REAL250005074035 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074035 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074035/0 /scratch/stefan/7916156/working/building/REAL250005074035 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 142) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/142 `/scratch/stefan/7916156/working/3D/142' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)CCC2CC2)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074035.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074035/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074035 none CC1(NC(=O)CCC2CC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [75, 42, 42, 7, 42, 3, 1, 1, 1, 1, 75, 75, 75, 184, 184, 201, 201, 201, 201, 201, 75, 75, 75, 75, 42, 7, 7, 3, 3, 1, 1, 1, 1, 1, 75, 75, 201, 75, 75] 201 rigid atoms, others: [32, 33, 6, 7, 8, 9, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 37, 38]) total number of confs: 596 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074035 none CC1(NC(=O)CCC2CC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 3, 19, 31, 75, 75, 1, 1, 1, 6, 6, 23, 23, 23, 23, 23, 1, 2, 2, 2, 3, 19, 19, 40, 40, 75, 75, 75, 75, 75, 1, 1, 24, 1, 1] 201 rigid atoms, others: [0, 1, 2, 35, 37, 38, 10, 11, 12, 34, 20] set([3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36]) total number of confs: 352 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074035 none CC1(NC(=O)CCC2CC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 24, 36, 36, 36, 125, 155, 201, 201, 23, 7, 1, 7, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 36, 125, 125, 160, 160, 201, 201, 201, 201, 201, 24, 23, 1, 24, 24] 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: 818 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074035 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074035 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074035/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074035 Building REAL250005074036 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074036' /scratch/stefan/7916156/working/building/REAL250005074036 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074036 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074036/0 /scratch/stefan/7916156/working/building/REAL250005074036 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 143) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/143 `/scratch/stefan/7916156/working/3D/143' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2CC=CC2)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074036.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074036/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074036 none CC1(NC(=O)C2CC=CC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [22, 12, 12, 1, 12, 1, 1, 1, 1, 1, 22, 22, 22, 57, 57, 70, 70, 70, 70, 70, 22, 22, 22, 22, 12, 1, 1, 1, 1, 1, 1, 1, 22, 22, 70, 22, 22] 70 rigid atoms, others: [3, 5, 6, 7, 8, 9, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36]) total number of confs: 194 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074036 none CC1(NC(=O)C2CC=CC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 3, 3, 3, 22, 22, 22, 22, 1, 1, 1, 6, 6, 22, 22, 22, 22, 22, 1, 2, 2, 2, 3, 22, 22, 22, 22, 22, 22, 22, 1, 1, 22, 1, 1] 70 rigid atoms, others: [0, 1, 2, 35, 36, 33, 32, 10, 11, 12, 20] set([3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34]) total number of confs: 89 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.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: REAL250005074036 none CC1(NC(=O)C2CC=CC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 31, 31, 31, 70, 70, 70, 70, 22, 8, 1, 8, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 31, 70, 70, 70, 70, 70, 70, 70, 22, 22, 1, 22, 22] 70 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: 181 number of broken/clashed sets: 6 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074036 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074036 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074036/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074036 Building REAL250005074037 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074037' /scratch/stefan/7916156/working/building/REAL250005074037 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074037 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074037/0 /scratch/stefan/7916156/working/building/REAL250005074037 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 144) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/144 `/scratch/stefan/7916156/working/3D/144' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)CC2CCC2)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074037.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074037/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074037 none CC1(NC(=O)CC2CCC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 136 conformations in input total number of sets (complete confs): 136 using faster count positions algorithm for large data unique positions, atoms: [53, 33, 33, 8, 33, 1, 1, 1, 1, 1, 53, 53, 53, 116, 116, 136, 136, 136, 136, 136, 53, 53, 53, 53, 33, 8, 8, 1, 1, 1, 1, 1, 1, 1, 53, 53, 136, 53, 53] 136 rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 34, 35, 36, 37, 38]) total number of confs: 398 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074037 none CC1(NC(=O)CC2CCC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 3, 22, 53, 53, 53, 1, 1, 1, 6, 6, 24, 24, 24, 24, 24, 1, 2, 2, 2, 3, 22, 22, 53, 53, 53, 53, 53, 53, 53, 1, 1, 24, 1, 1] 136 rigid atoms, others: [0, 1, 2, 35, 37, 38, 10, 11, 12, 34, 20] set([3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074037 none CC1(NC(=O)CC2CCC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 136 conformations in input total number of sets (complete confs): 136 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 24, 39, 39, 39, 103, 136, 136, 136, 24, 8, 1, 8, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 39, 103, 103, 136, 136, 136, 136, 136, 136, 136, 24, 24, 1, 24, 24] 136 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: 507 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074037 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074037 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074037/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074037 Building REAL250005074038 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074038' /scratch/stefan/7916156/working/building/REAL250005074038 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074038 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074038/0 /scratch/stefan/7916156/working/building/REAL250005074038 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 145) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/145 `/scratch/stefan/7916156/working/3D/145' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1)C1CC1) `REAL250005074038.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074038/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074038 none CC(C(=O)NC1(C)CN(C(=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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [59, 16, 16, 16, 14, 14, 14, 13, 6, 1, 6, 1, 1, 1, 1, 1, 1, 14, 59, 60, 60, 59, 59, 59, 59, 16, 14, 14, 14, 13, 14, 1, 14, 14, 60, 60, 60, 60, 60] 60 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: 207 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074038 none CC(C(=O)NC1(C)CN(C(=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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [16, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 13, 13, 13, 13, 13, 1, 16, 17, 17, 16, 16, 16, 16, 3, 2, 2, 2, 1, 1, 14, 1, 1, 17, 17, 17, 17, 17] 60 rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 9, 17, 29, 30] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 34, 35, 36, 37, 38]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074038 none CC(C(=O)NC1(C)CN(C(=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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 1, 3, 12, 12, 12, 17, 17, 17, 17, 48, 48, 60, 60, 60, 60, 60, 17, 1, 1, 1, 3, 3, 3, 3, 12, 17, 17, 17, 17, 17, 60, 17, 17, 1, 1, 1, 1, 1] 60 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: 163 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074038 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074038 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074038/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074038 Building REAL250005074039 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074039' /scratch/stefan/7916156/working/building/REAL250005074039 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074039 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074039/0 /scratch/stefan/7916156/working/building/REAL250005074039 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 146) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/146 `/scratch/stefan/7916156/working/3D/146' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=C(C)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074039.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074039/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074039 none CC=C(C)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 24, 56, 24, 24, 17, 17, 17, 17, 8, 1, 8, 1, 1, 1, 1, 1, 1, 17, 56, 56, 56, 56, 56, 56, 56, 24, 17, 17, 17, 17, 17, 1, 17, 17] 56 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: 151 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074039 none CC=C(C)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 3, 18, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 17, 17, 17, 17, 17, 1, 18, 18, 18, 18, 18, 18, 18, 3, 2, 2, 2, 1, 1, 17, 1, 1] 56 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074039 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074039 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074039/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074039 Building REAL250005074040 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074040' /scratch/stefan/7916156/working/building/REAL250005074040 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074040 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074040/0 /scratch/stefan/7916156/working/building/REAL250005074040 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 147) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/147 `/scratch/stefan/7916156/working/3D/147' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC(C(=O)NC2(C)CN(C(=O)C3=CC(=O)[N-]O3)C2)C1) `REAL250005074040.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074040.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074040/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074040 none CC1CC(C(=O)NC2(C)CN(C(=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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 3, 3, 3, 1, 1, 1, 1, 1, 1, 7, 7, 16, 16, 16, 16, 16, 1, 17, 17, 17, 17, 17, 17, 17, 17, 3, 2, 2, 2, 1, 1, 16, 1, 1, 17, 17] 55 rigid atoms, others: [32, 33, 35, 36, 6, 7, 8, 9, 10, 11, 19] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 37, 38]) total number of confs: 72 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074040 none CC1CC(C(=O)NC2(C)CN(C(=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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 11, 11, 11, 17, 17, 17, 17, 49, 49, 55, 55, 55, 55, 55, 17, 1, 2, 2, 2, 1, 1, 1, 1, 11, 17, 17, 17, 17, 17, 55, 17, 17, 1, 1] 55 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: 156 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.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: REAL250005074040 none CC1CC(C(=O)NC2(C)CN(C(=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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 55, 23, 23, 23, 16, 16, 16, 16, 8, 1, 8, 1, 1, 1, 1, 1, 1, 16, 55, 55, 55, 55, 55, 55, 55, 55, 23, 16, 16, 16, 16, 16, 1, 16, 16, 55, 55] 55 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: 155 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074040 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074040 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074040/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074040 Building REAL250005074041 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074041' /scratch/stefan/7916156/working/building/REAL250005074041 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074041 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074041/0 /scratch/stefan/7916156/working/building/REAL250005074041 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 148) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/148 `/scratch/stefan/7916156/working/3D/148' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C=C2CCC2)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074041.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074041/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074041 none CC1(NC(=O)C=C2CCC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [21, 10, 10, 1, 10, 1, 1, 1, 1, 1, 21, 21, 21, 60, 60, 72, 72, 72, 72, 72, 21, 21, 21, 21, 10, 1, 1, 1, 1, 1, 1, 1, 21, 21, 72, 21, 21] 72 rigid atoms, others: [3, 5, 6, 7, 8, 9, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36]) total number of confs: 196 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074041 none CC1(NC(=O)C=C2CCC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 3, 3, 3, 21, 21, 21, 21, 1, 1, 1, 6, 6, 18, 18, 18, 18, 18, 1, 2, 2, 2, 3, 21, 21, 21, 21, 21, 21, 21, 1, 1, 18, 1, 1] 72 rigid atoms, others: [0, 1, 2, 35, 36, 33, 32, 10, 11, 12, 20] set([3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34]) 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.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: REAL250005074041 none CC1(NC(=O)C=C2CCC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 18, 27, 27, 27, 72, 72, 72, 72, 18, 8, 1, 8, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 27, 72, 72, 72, 72, 72, 72, 72, 18, 18, 1, 18, 18] 72 rigid atoms, others: [34, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36]) total number of confs: 196 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074041 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074041 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074041/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074041 Building REAL250005074042 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074042' /scratch/stefan/7916156/working/building/REAL250005074042 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074042 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074042/0 /scratch/stefan/7916156/working/building/REAL250005074042 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 149) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/149 `/scratch/stefan/7916156/working/3D/149' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)=C(F)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074042.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074042/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074042 none CC(C)=C(F)C(=O)NC1(C)CN(C(=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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 22, 42, 22, 22, 15, 15, 15, 15, 7, 1, 7, 1, 1, 1, 1, 1, 1, 15, 42, 42, 42, 42, 42, 42, 22, 15, 15, 15, 15, 15, 1, 15, 15] 42 rigid atoms, others: [33, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35]) total number of confs: 120 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074042 none CC(C)=C(F)C(=O)NC1(C)CN(C(=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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 3, 13, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 15, 15, 15, 15, 15, 1, 13, 13, 13, 13, 13, 13, 3, 2, 2, 2, 1, 1, 15, 1, 1] 42 rigid atoms, others: [32, 34, 35, 7, 8, 9, 10, 11, 12, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074042 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074042 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074042/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074042 Building REAL250005074043 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074043' /scratch/stefan/7916156/working/building/REAL250005074043 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074043 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074043/0 /scratch/stefan/7916156/working/building/REAL250005074043 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 150) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/150 `/scratch/stefan/7916156/working/3D/150' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CCCC2)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074043.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074043.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074043/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074043 none CC1(NC(=O)C2=CCCC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [12, 8, 8, 1, 8, 1, 1, 1, 1, 1, 12, 12, 12, 30, 30, 37, 37, 37, 37, 37, 12, 12, 12, 12, 8, 1, 1, 1, 1, 1, 1, 1, 12, 12, 37, 12, 12] 37 rigid atoms, others: [3, 5, 6, 7, 8, 9, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36]) total number of confs: 104 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074043 none CC1(NC(=O)C2=CCCC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 3, 3, 3, 12, 12, 12, 12, 1, 1, 1, 6, 6, 15, 15, 15, 15, 15, 1, 2, 2, 2, 3, 12, 12, 12, 12, 12, 12, 12, 1, 1, 15, 1, 1] 37 rigid atoms, others: [0, 1, 2, 35, 36, 33, 32, 10, 11, 12, 20] set([3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074043 none CC1(NC(=O)C2=CCCC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 25, 25, 25, 37, 37, 37, 37, 15, 6, 1, 6, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 25, 37, 37, 37, 37, 37, 37, 37, 15, 15, 1, 15, 15] 37 rigid atoms, others: [34, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36]) total number of confs: 90 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074043 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074043 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074043/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074043 Building REAL250005074044 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074044' /scratch/stefan/7916156/working/building/REAL250005074044 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074044 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074044/0 /scratch/stefan/7916156/working/building/REAL250005074044 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 151) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/151 `/scratch/stefan/7916156/working/3D/151' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CC1C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074044.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074044.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074044/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074044 none CC1(C)CC1C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 2, 2, 2, 1, 1, 1, 1, 1, 1, 6, 6, 17, 17, 17, 17, 17, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 2, 1, 1, 17, 1, 1] 47 rigid atoms, others: [34, 35, 37, 38, 7, 8, 9, 10, 11, 12, 20] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36]) total number of confs: 69 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074044 none CC1(C)CC1C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 9, 9, 9, 15, 15, 15, 15, 39, 39, 47, 47, 47, 47, 47, 15, 1, 1, 1, 2, 2, 2, 1, 1, 1, 9, 15, 15, 15, 15, 15, 47, 15, 15] 47 rigid atoms, others: [0, 1, 2, 3, 4, 5, 21, 22, 23, 27, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074044 none CC1(C)CC1C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 47, 22, 22, 22, 17, 17, 17, 17, 8, 1, 8, 1, 1, 1, 1, 1, 1, 17, 47, 47, 47, 47, 47, 47, 47, 47, 47, 22, 17, 17, 17, 17, 17, 1, 17, 17] 47 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: 129 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074044 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074044 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074044/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074044 Building REAL250005074045 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074045' /scratch/stefan/7916156/working/building/REAL250005074045 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074045 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074045/0 /scratch/stefan/7916156/working/building/REAL250005074045 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 152) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/152 `/scratch/stefan/7916156/working/3D/152' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)C[C@@H]1C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074045.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074045/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074045 none CC1(C)C[C@@H]1C(=O)NC1(C)CN(C(=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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 3, 15, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 17, 17, 17, 17, 17, 1, 15, 15, 15, 15, 15, 15, 15, 15, 3, 2, 2, 2, 1, 1, 17, 1, 1] 47 rigid atoms, others: [34, 35, 37, 38, 8, 9, 10, 11, 12, 13, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36]) total number of confs: 68 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074045 none CC1(C)C[C@@H]1C(=O)NC1(C)CN(C(=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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 15, 15, 15, 15, 39, 39, 47, 47, 47, 47, 47, 15, 2, 2, 2, 2, 2, 2, 1, 1, 9, 15, 15, 15, 15, 15, 47, 15, 15] 47 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.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: REAL250005074045 none CC1(C)C[C@@H]1C(=O)NC1(C)CN(C(=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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 47, 22, 47, 22, 22, 18, 18, 18, 17, 8, 1, 8, 1, 1, 1, 1, 1, 1, 18, 47, 47, 47, 47, 47, 47, 47, 47, 22, 18, 18, 18, 17, 17, 1, 18, 18] 47 rigid atoms, others: [36, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 125 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074045 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074045 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074045/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074045 Building REAL250005074046 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074046' /scratch/stefan/7916156/working/building/REAL250005074046 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074046 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074046/0 /scratch/stefan/7916156/working/building/REAL250005074046 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 153) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/153 `/scratch/stefan/7916156/working/3D/153' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)[C@@H]2CCCO2)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074046.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074046/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074046 none CC1(NC(=O)[C@@H]2CCCO2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [21, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 21, 21, 21, 57, 57, 75, 75, 75, 75, 75, 21, 21, 21, 21, 12, 1, 1, 1, 1, 1, 1, 21, 21, 75, 21, 21] 75 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 32, 33, 34, 35, 36]) total number of confs: 194 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074046 none CC1(NC(=O)[C@@H]2CCCO2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 3, 3, 3, 21, 21, 21, 21, 21, 1, 1, 1, 6, 6, 24, 24, 24, 24, 24, 1, 2, 2, 2, 3, 21, 21, 21, 21, 21, 21, 1, 1, 25, 1, 1] 75 rigid atoms, others: [0, 1, 2, 35, 36, 33, 32, 11, 12, 13, 21] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34]) total number of confs: 91 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.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: REAL250005074046 none CC1(NC(=O)[C@@H]2CCCO2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [25, 25, 25, 36, 36, 36, 75, 75, 75, 75, 75, 24, 9, 1, 9, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 36, 75, 75, 75, 75, 75, 75, 24, 25, 1, 25, 25] 75 rigid atoms, others: [34, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36]) total number of confs: 203 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074046 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074046 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074046/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074046 Building REAL250005074047 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074047' /scratch/stefan/7916156/working/building/REAL250005074047 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074047 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074047/0 /scratch/stefan/7916156/working/building/REAL250005074047 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 154) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/154 `/scratch/stefan/7916156/working/3D/154' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074047.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074047/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074047 none CCC(C)CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 173 conformations in input total number of sets (complete confs): 173 using faster count positions algorithm for large data unique positions, atoms: [173, 165, 131, 163, 31, 31, 31, 25, 25, 25, 25, 11, 1, 11, 1, 1, 1, 1, 1, 1, 25, 173, 173, 173, 173, 173, 165, 165, 165, 165, 131, 131, 31, 25, 25, 25, 25, 25, 1, 25, 25] 173 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: 688 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074047 none CCC(C)CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 173 conformations in input total number of sets (complete confs): 173 using faster count positions algorithm for large data unique positions, atoms: [78, 51, 22, 50, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 25, 25, 25, 25, 25, 1, 78, 78, 78, 77, 78, 52, 52, 52, 52, 22, 22, 3, 2, 2, 2, 1, 1, 25, 1, 1] 173 rigid atoms, others: [36, 37, 7, 8, 9, 10, 11, 12, 40, 20, 39] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38]) total number of confs: 407 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074047 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074047 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074047/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074047 Building REAL250005074048 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074048' /scratch/stefan/7916156/working/building/REAL250005074048 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074048 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074048/0 /scratch/stefan/7916156/working/building/REAL250005074048 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 155) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/155 `/scratch/stefan/7916156/working/3D/155' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074048.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074048.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074048/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074048 none C#CCCCC(=O)NC1(C)CN(C(=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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 136, 108, 21, 21, 21, 17, 17, 17, 16, 5, 1, 5, 1, 1, 1, 1, 1, 1, 17, 201, 190, 193, 157, 157, 108, 108, 21, 17, 17, 17, 17, 16, 1, 17, 17] 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: 945 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074048 none C#CCCCC(=O)NC1(C)CN(C(=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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [91, 91, 32, 19, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 16, 16, 16, 16, 16, 1, 91, 82, 83, 42, 42, 19, 19, 3, 2, 2, 2, 1, 1, 17, 1, 1] 201 rigid atoms, others: [32, 33, 35, 36, 7, 8, 9, 10, 11, 12, 20] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34]) total number of confs: 448 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074048 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074048 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074048/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074048 Building REAL250005074049 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074049' /scratch/stefan/7916156/working/building/REAL250005074049 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074049 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074049/0 /scratch/stefan/7916156/working/building/REAL250005074049 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 156) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/156 `/scratch/stefan/7916156/working/3D/156' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(O)CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074049.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074049/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074049 none CC(C)(O)CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 198 conformations in input total number of sets (complete confs): 198 using faster count positions algorithm for large data unique positions, atoms: [66, 56, 64, 66, 24, 24, 24, 19, 19, 19, 19, 6, 1, 6, 1, 1, 1, 1, 1, 1, 19, 66, 66, 66, 66, 66, 66, 198, 56, 56, 24, 19, 19, 19, 19, 18, 1, 19, 19] 198 rigid atoms, others: [36, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 445 number of broken/clashed sets: 13 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074049 none CC(C)(O)CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 198 conformations in input total number of sets (complete confs): 198 using faster count positions algorithm for large data unique positions, atoms: [28, 17, 27, 30, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 18, 18, 19, 18, 18, 1, 30, 30, 30, 30, 30, 30, 90, 17, 17, 3, 2, 2, 2, 1, 1, 19, 1, 1] 198 rigid atoms, others: [34, 35, 37, 38, 7, 8, 9, 10, 11, 12, 20] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36]) total number of confs: 268 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074049 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074049 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074049/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074049 Building REAL250005074050 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074050' /scratch/stefan/7916156/working/building/REAL250005074050 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074050 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074050/0 /scratch/stefan/7916156/working/building/REAL250005074050 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 157) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/157 `/scratch/stefan/7916156/working/3D/157' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](O)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074050.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074050/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074050 none CC(C)[C@@H](O)C(=O)NC1(C)CN(C(=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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 198 conformations in input total number of sets (complete confs): 198 using faster count positions algorithm for large data unique positions, atoms: [66, 54, 64, 26, 54, 54, 26, 26, 22, 22, 22, 22, 9, 1, 9, 1, 1, 1, 1, 1, 1, 22, 66, 66, 66, 66, 66, 66, 66, 162, 26, 22, 22, 22, 22, 22, 1, 22, 22] 198 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: 423 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074050 none CC(C)[C@@H](O)C(=O)NC1(C)CN(C(=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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 198 conformations in input total number of sets (complete confs): 198 using faster count positions algorithm for large data unique positions, atoms: [29, 15, 27, 3, 15, 15, 2, 3, 1, 1, 1, 1, 1, 1, 6, 6, 22, 22, 22, 22, 22, 1, 29, 29, 29, 29, 29, 29, 29, 45, 2, 2, 2, 2, 1, 1, 22, 1, 1] 198 rigid atoms, others: [34, 35, 37, 38, 8, 9, 10, 11, 12, 13, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36]) total number of confs: 211 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074050 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074050 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074050/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074050 Building REAL250005074051 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074051' /scratch/stefan/7916156/working/building/REAL250005074051 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074051 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074051/0 /scratch/stefan/7916156/working/building/REAL250005074051 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 158) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/158 `/scratch/stefan/7916156/working/3D/158' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)=CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074051.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074051/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074051 none CCC(C)=CC(=O)NC1(C)CN(C(=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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 92 conformations in input total number of sets (complete confs): 92 using faster count positions algorithm for large data unique positions, atoms: [92, 49, 49, 49, 27, 27, 27, 19, 19, 19, 18, 8, 1, 8, 1, 1, 1, 1, 1, 1, 19, 92, 92, 92, 92, 92, 49, 49, 49, 49, 27, 19, 19, 19, 19, 18, 1, 19, 19] 92 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: 398 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074051 none CCC(C)=CC(=O)NC1(C)CN(C(=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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 92 conformations in input total number of sets (complete confs): 92 using faster count positions algorithm for large data unique positions, atoms: [24, 13, 13, 13, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 18, 18, 18, 18, 18, 1, 24, 24, 24, 24, 24, 13, 13, 13, 13, 3, 2, 2, 2, 1, 1, 19, 1, 1] 92 rigid atoms, others: [34, 35, 37, 38, 7, 8, 9, 10, 11, 12, 20] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074051 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074051 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074051/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074051 Building REAL250005074052 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074052' /scratch/stefan/7916156/working/building/REAL250005074052 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074052 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074052/0 /scratch/stefan/7916156/working/building/REAL250005074052 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 159) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/159 `/scratch/stefan/7916156/working/3D/159' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C#CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074052.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074052.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074052/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074052 none CC(C)C#CC(=O)NC1(C)CN(C(=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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 14, 14, 9, 9, 9, 8, 3, 1, 3, 1, 1, 1, 1, 1, 1, 9, 14, 14, 14, 14, 14, 14, 14, 14, 9, 9, 9, 9, 8, 1, 9, 9] 14 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: 37 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074052 none CC(C)C#CC(=O)NC1(C)CN(C(=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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 8, 8, 8, 8, 8, 1, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 1, 1, 9, 1, 1] 14 rigid atoms, others: [32, 33, 35, 36, 7, 8, 9, 10, 11, 12, 20] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34]) total number of confs: 30 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074052 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074052 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074052/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074052 Building REAL250005074053 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074053' /scratch/stefan/7916156/working/building/REAL250005074053 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074053 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074053/0 /scratch/stefan/7916156/working/building/REAL250005074053 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 160) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/160 `/scratch/stefan/7916156/working/3D/160' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C#CC2CC2)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074053.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074053.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074053/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074053 none CC1(NC(=O)C#CC2CC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 13, 13, 16, 16, 16, 16, 16, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 3, 3, 16, 3, 3] 16 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 24, 25, 26, 27, 28, 29] set([0, 32, 34, 33, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31]) total number of confs: 36 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074053 none CC1(NC(=O)C#CC2CC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 6, 6, 10, 10, 10, 10, 10, 1, 2, 2, 2, 3, 3, 3, 3, 3, 3, 1, 1, 10, 1, 1] 16 rigid atoms, others: [0, 1, 2, 33, 10, 11, 12, 34, 20, 30, 31] set([3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32]) 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.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: REAL250005074053 none CC1(NC(=O)C#CC2CC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [10, 10, 10, 16, 16, 16, 16, 16, 16, 16, 10, 4, 1, 4, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 16, 16, 16, 16, 16, 16, 10, 10, 1, 10, 10] 16 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: 41 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074053 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074053 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074053/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074053 Building REAL250005074054 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074054' /scratch/stefan/7916156/working/building/REAL250005074054 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074054 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074054/0 /scratch/stefan/7916156/working/building/REAL250005074054 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 161) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/161 `/scratch/stefan/7916156/working/3D/161' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)CCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074054.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074054/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074054 none C=C(C)CCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 134 conformations in input total number of sets (complete confs): 134 using faster count positions algorithm for large data unique positions, atoms: [134, 133, 134, 108, 31, 31, 31, 24, 24, 24, 23, 11, 1, 11, 1, 1, 1, 1, 1, 1, 24, 134, 134, 134, 134, 134, 133, 133, 108, 108, 31, 24, 24, 24, 24, 23, 1, 24, 24] 134 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: 520 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074054 none C=C(C)CCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 134 conformations in input total number of sets (complete confs): 134 using faster count positions algorithm for large data unique positions, atoms: [61, 35, 61, 18, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 23, 23, 23, 23, 23, 1, 61, 61, 61, 61, 61, 35, 35, 18, 18, 3, 2, 2, 2, 1, 1, 24, 1, 1] 134 rigid atoms, others: [34, 35, 37, 38, 7, 8, 9, 10, 11, 12, 20] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36]) total number of confs: 275 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074054 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074054 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074054/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074054 Building REAL250005074055 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074055' /scratch/stefan/7916156/working/building/REAL250005074055 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074055 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074055/0 /scratch/stefan/7916156/working/building/REAL250005074055 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 162) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/162 `/scratch/stefan/7916156/working/3D/162' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)[C@H]2CCCO2)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074055.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074055/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074055 none CC1(NC(=O)[C@H]2CCCO2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [19, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 19, 19, 19, 56, 56, 73, 73, 73, 73, 73, 19, 19, 19, 19, 11, 1, 1, 1, 1, 1, 1, 19, 19, 73, 19, 19] 73 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 32, 33, 34, 35, 36]) total number of confs: 190 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074055 none CC1(NC(=O)[C@H]2CCCO2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 3, 3, 3, 19, 19, 19, 19, 19, 1, 1, 1, 6, 6, 23, 23, 23, 23, 23, 1, 2, 2, 2, 3, 19, 19, 19, 19, 19, 19, 1, 1, 23, 1, 1] 73 rigid atoms, others: [0, 1, 2, 35, 36, 33, 32, 11, 12, 13, 21] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34]) total number of confs: 84 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.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: REAL250005074055 none CC1(NC(=O)[C@H]2CCCO2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [23, 23, 23, 36, 36, 36, 73, 73, 73, 73, 73, 23, 10, 1, 10, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 36, 73, 73, 73, 73, 73, 73, 23, 23, 1, 23, 23] 73 rigid atoms, others: [34, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36]) total number of confs: 202 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074055 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074055 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074055/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074055 Building REAL250005074056 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074056' /scratch/stefan/7916156/working/building/REAL250005074056 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005074056 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074056/0 /scratch/stefan/7916156/working/building/REAL250005074056 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 163) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/163 `/scratch/stefan/7916156/working/3D/163' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=NNN=C2)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074056.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074056/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074056 none CC1(NC(=O)C2=NNN=C2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 8, 8, 8, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 5, 1, 5, 1, 1, 1, 1, 1, 9, 9, 9, 19, 19, 22, 22, 22, 22, 22, 9, 9, 9, 9, 6, 1, 1, 9, 9, 22, 9, 9] 22 rigid atoms, others: [3, 5, 6, 7, 8, 9, 25, 26] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31]) total number of confs: 57 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074056 none CC1(NC(=O)C2=NNN=C2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 8, 8, 8, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 1, 1, 1, 6, 6, 16, 16, 16, 16, 16, 1, 2, 2, 2, 3, 9, 9, 1, 1, 16, 1, 1] 22 rigid atoms, others: [0, 1, 2, 10, 11, 12, 20, 27, 28, 30, 31] set([3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 29]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074056 none CC1(NC(=O)C2=NNN=C2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 8, 8, 8, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [16, 16, 16, 19, 19, 19, 22, 22, 22, 22, 16, 9, 1, 9, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 19, 22, 22, 16, 16, 1, 16, 16] 22 rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31]) total number of confs: 46 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074056 /scratch/stefan/7916156/working /scratch/stefan/7916156 mkdir: created directory `1' /scratch/stefan/7916156/working/building/REAL250005074056/1 /scratch/stefan/7916156/working/building/REAL250005074056 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 1 (index: 164) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/164 `/scratch/stefan/7916156/working/3D/164' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CN=NN2)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074056.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005074056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074056/1/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074056 none CC1(NC(=O)C2=CN=NN2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 8, 8, 8, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [15, 9, 9, 1, 9, 1, 1, 1, 1, 1, 15, 15, 15, 29, 29, 31, 31, 31, 31, 31, 15, 15, 15, 15, 9, 1, 1, 15, 15, 31, 15, 15] 31 rigid atoms, others: [3, 5, 6, 7, 8, 9, 25, 26] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31]) total number of confs: 93 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074056 none CC1(NC(=O)C2=CN=NN2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 8, 8, 8, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 3, 3, 3, 15, 15, 15, 15, 1, 1, 1, 6, 6, 11, 11, 11, 11, 11, 1, 2, 2, 2, 3, 15, 15, 1, 1, 11, 1, 1] 31 rigid atoms, others: [0, 1, 2, 10, 11, 12, 20, 27, 28, 30, 31] set([3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 29]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074056 none CC1(NC(=O)C2=CN=NN2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 8, 8, 8, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 18, 18, 18, 31, 31, 31, 31, 11, 6, 1, 6, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 18, 31, 31, 11, 11, 1, 11, 11] 31 rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31]) total number of confs: 69 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074056 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074056 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 1: /scratch/stefan/7916156/working/building/REAL250005074056/1.* 0: /scratch/stefan/7916156/working/building/REAL250005074056/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074056 Building REAL250005074057 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074057' /scratch/stefan/7916156/working/building/REAL250005074057 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074057 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074057/0 /scratch/stefan/7916156/working/building/REAL250005074057 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 165) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/165 `/scratch/stefan/7916156/working/3D/165' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(CC(=O)NC2(C)CN(C(=O)C3=CC(=O)[N-]O3)C2)CC1) `REAL250005074057.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074057/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074057 none CC1(CC(=O)NC2(C)CN(C(=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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 113 conformations in input total number of sets (complete confs): 113 using faster count positions algorithm for large data unique positions, atoms: [40, 22, 2, 2, 2, 1, 1, 1, 1, 1, 1, 6, 6, 18, 18, 18, 18, 18, 1, 40, 40, 40, 40, 40, 22, 22, 2, 2, 2, 2, 1, 1, 18, 1, 1, 40, 40, 40, 40] 113 rigid atoms, others: [33, 34, 5, 6, 7, 8, 9, 10, 18, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 35, 36, 37, 38]) total number of confs: 164 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074057 none CC1(CC(=O)NC2(C)CN(C(=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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 7, 28, 28, 28, 40, 40, 40, 40, 96, 96, 113, 113, 113, 113, 113, 40, 1, 1, 2, 2, 2, 7, 7, 28, 40, 40, 40, 40, 40, 113, 40, 40, 1, 1, 1, 1] 113 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: 339 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074057 none CC1(CC(=O)NC2(C)CN(C(=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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 113 conformations in input total number of sets (complete confs): 113 using faster count positions algorithm for large data unique positions, atoms: [113, 103, 23, 23, 23, 18, 18, 18, 18, 8, 1, 8, 1, 1, 1, 1, 1, 1, 18, 113, 113, 113, 113, 113, 103, 103, 23, 18, 18, 18, 18, 18, 1, 18, 18, 113, 113, 113, 113] 113 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: 374 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074057 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074057 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074057/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074057 Building REAL250005074058 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074058' /scratch/stefan/7916156/working/building/REAL250005074058 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074058 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074058/0 /scratch/stefan/7916156/working/building/REAL250005074058 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 166) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/166 `/scratch/stefan/7916156/working/3D/166' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CN=CO2)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074058.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074058/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074058 none CC1(NC(=O)C2=CN=CO2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 8, 1, 12, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 6, 1, 6, 1, 1, 1, 1, 1, 10, 10, 10, 24, 24, 26, 26, 26, 26, 26, 10, 10, 10, 10, 6, 1, 1, 10, 10, 26, 10, 10] 26 rigid atoms, others: [3, 5, 6, 7, 8, 9, 25, 26] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31]) total number of confs: 67 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074058 none CC1(NC(=O)C2=CN=CO2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 8, 1, 12, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 1, 1, 1, 6, 6, 15, 15, 15, 15, 15, 1, 2, 2, 2, 3, 10, 10, 1, 1, 15, 1, 1] 26 rigid atoms, others: [0, 1, 2, 10, 11, 12, 20, 27, 28, 30, 31] set([3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 29]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074058 none CC1(NC(=O)C2=CN=CO2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 8, 1, 12, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 15, 15, 17, 17, 17, 26, 26, 26, 26, 15, 8, 1, 8, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 17, 26, 26, 15, 15, 1, 15, 15] 26 rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31]) total number of confs: 50 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074058 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074058 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074058/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074058 Building REAL250005074059 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074059' /scratch/stefan/7916156/working/building/REAL250005074059 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074059 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074059/0 /scratch/stefan/7916156/working/building/REAL250005074059 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 167) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/167 `/scratch/stefan/7916156/working/3D/167' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H]1C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074059.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074059/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074059 none C[C@@H]1C[C@H]1C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 21, 3, 21, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 17, 17, 17, 17, 17, 1, 21, 21, 21, 21, 21, 3, 2, 2, 2, 1, 1, 17, 1, 1] 56 rigid atoms, others: [32, 34, 35, 8, 9, 10, 11, 12, 13, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33]) total number of confs: 81 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074059 none C[C@@H]1C[C@H]1C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 21, 21, 21, 21, 48, 48, 56, 56, 56, 56, 56, 21, 2, 2, 2, 1, 1, 12, 21, 21, 21, 21, 21, 56, 21, 21] 56 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 25, 26] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.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: REAL250005074059 none C[C@@H]1C[C@H]1C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 56, 56, 23, 56, 23, 23, 18, 18, 18, 17, 7, 1, 7, 1, 1, 1, 1, 1, 1, 18, 56, 56, 56, 56, 56, 23, 18, 18, 18, 17, 17, 1, 18, 18] 56 rigid atoms, others: [33, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35]) total number of confs: 156 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074059 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074059 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074059/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074059 Building REAL250005074060 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074060' /scratch/stefan/7916156/working/building/REAL250005074060 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074060 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074060/0 /scratch/stefan/7916156/working/building/REAL250005074060 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 168) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/168 `/scratch/stefan/7916156/working/3D/168' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(F)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074060.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074060/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074060 none CCC(F)C(=O)NC1(C)CN(C(=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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [81, 73, 35, 73, 35, 35, 25, 25, 25, 25, 9, 1, 9, 1, 1, 1, 1, 1, 1, 25, 81, 81, 81, 81, 81, 73, 35, 25, 25, 25, 25, 25, 1, 25, 25] 81 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: 300 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074060 none CCC(F)C(=O)NC1(C)CN(C(=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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [33, 22, 3, 22, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 25, 25, 25, 25, 25, 1, 39, 39, 39, 39, 39, 22, 3, 2, 2, 2, 1, 1, 25, 1, 1] 81 rigid atoms, others: [33, 34, 6, 7, 8, 9, 10, 11, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32]) total number of confs: 236 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074060 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074060 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074060/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074060 Building REAL250005074061 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074061' /scratch/stefan/7916156/working/building/REAL250005074061 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074061 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074061/0 /scratch/stefan/7916156/working/building/REAL250005074061 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 169) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/169 `/scratch/stefan/7916156/working/3D/169' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)CCCF)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074061.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074061.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074061/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074061 none CC1(NC(=O)CCCF)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 15, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 23, 36, 36, 36, 158, 186, 201, 22, 6, 1, 6, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 36, 158, 158, 201, 201, 201, 201, 23, 22, 1, 23, 23] 201 rigid atoms, others: [32, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34]) total number of confs: 900 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074061 none CC1(NC(=O)CCCF)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 15, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 3, 19, 35, 87, 1, 1, 1, 6, 6, 22, 22, 22, 22, 22, 1, 2, 2, 2, 3, 19, 19, 43, 43, 84, 84, 1, 1, 23, 1, 1] 201 rigid atoms, others: [0, 1, 2, 33, 9, 10, 11, 34, 19, 30, 31] set([3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32]) total number of confs: 449 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074061 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074061 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074061/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074061 Building REAL250005074062 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074062' /scratch/stefan/7916156/working/building/REAL250005074062 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074062 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074062/0 /scratch/stefan/7916156/working/building/REAL250005074062 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 170) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/170 `/scratch/stefan/7916156/working/3D/170' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@@H]1C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074062.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074062/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074062 none C[C@H]1C[C@@H]1C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [21, 21, 21, 21, 3, 21, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 19, 19, 19, 19, 19, 1, 21, 21, 21, 21, 21, 3, 2, 2, 2, 1, 1, 20, 1, 1] 58 rigid atoms, others: [32, 34, 35, 8, 9, 10, 11, 12, 13, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33]) total number of confs: 86 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074062 none C[C@H]1C[C@@H]1C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 21, 21, 21, 21, 50, 50, 58, 58, 58, 58, 58, 21, 2, 2, 2, 1, 1, 12, 21, 21, 21, 21, 21, 58, 21, 21] 58 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 25, 26] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074062 none C[C@H]1C[C@@H]1C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 58, 58, 25, 58, 25, 25, 20, 20, 20, 19, 7, 1, 7, 1, 1, 1, 1, 1, 1, 20, 58, 58, 58, 58, 58, 25, 20, 20, 20, 19, 19, 1, 20, 20] 58 rigid atoms, others: [33, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35]) total number of confs: 158 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074062 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074062 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074062/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074062 Building REAL250005074063 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074063' /scratch/stefan/7916156/working/building/REAL250005074063 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074063 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074063/0 /scratch/stefan/7916156/working/building/REAL250005074063 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 171) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/171 `/scratch/stefan/7916156/working/3D/171' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(F)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074063.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074063/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074063 none CC(C)C(F)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 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', '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, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [61, 45, 61, 21, 45, 21, 21, 19, 19, 19, 19, 10, 1, 10, 1, 1, 1, 1, 1, 1, 19, 61, 61, 61, 61, 61, 61, 61, 45, 21, 19, 19, 19, 19, 19, 1, 19, 19] 61 rigid atoms, others: [35, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37]) total number of confs: 241 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074063 none CC(C)C(F)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 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', '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, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [22, 13, 23, 3, 13, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 19, 19, 19, 19, 19, 1, 23, 23, 23, 23, 23, 23, 23, 13, 3, 2, 2, 2, 1, 1, 19, 1, 1] 61 rigid atoms, others: [33, 34, 36, 37, 7, 8, 9, 10, 11, 12, 20] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074063 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074063 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074063/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074063 Building REAL250005074064 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074064' /scratch/stefan/7916156/working/building/REAL250005074064 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074064 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074064/0 /scratch/stefan/7916156/working/building/REAL250005074064 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 172) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/172 `/scratch/stefan/7916156/working/3D/172' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074064.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074064/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074064 none C=CCCCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 115, 98, 18, 18, 18, 15, 15, 15, 14, 5, 1, 5, 1, 1, 1, 1, 1, 1, 15, 201, 201, 201, 185, 186, 139, 139, 98, 98, 18, 15, 15, 15, 15, 14, 1, 15, 15] 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: 911 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074064 none C=CCCCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [126, 81, 32, 19, 3, 3, 3, 1, 1, 1, 1, 1, 1, 5, 5, 14, 14, 14, 14, 14, 1, 126, 126, 126, 73, 73, 40, 40, 19, 19, 3, 2, 2, 2, 1, 1, 15, 1, 1] 201 rigid atoms, others: [34, 35, 37, 38, 7, 8, 9, 10, 11, 12, 20] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36]) total number of confs: 563 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074064 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074064 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074064/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074064 Building REAL250005074065 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074065' /scratch/stefan/7916156/working/building/REAL250005074065 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074065 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074065/0 /scratch/stefan/7916156/working/building/REAL250005074065 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 173) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/173 `/scratch/stefan/7916156/working/3D/173' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C(N)=O)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074065.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074065.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074065/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074065 none CC1(NC(=O)C(N)=O)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.am', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 8, 11, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 4, 6, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 29, 29, 29, 38, 38, 18, 10, 1, 10, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 29, 38, 38, 18, 18, 1, 18, 18] 38 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29]) total number of confs: 107 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074065 none CC1(NC(=O)C(N)=O)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.am', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 8, 11, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 4, 6, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 3, 3, 3, 12, 13, 1, 1, 1, 6, 6, 18, 18, 18, 18, 18, 1, 2, 2, 2, 3, 13, 12, 1, 1, 18, 1, 1] 38 rigid atoms, others: [0, 1, 2, 8, 9, 10, 18, 25, 26, 28, 29] set([3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 27]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074065 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074065 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074065/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074065 Building REAL250005074066 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074066' /scratch/stefan/7916156/working/building/REAL250005074066 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074066 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074066/0 /scratch/stefan/7916156/working/building/REAL250005074066 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 174) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/174 `/scratch/stefan/7916156/working/3D/174' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC1CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074066.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074066/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074066 none CC1CC1CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 155 conformations in input total number of sets (complete confs): 155 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 54, 24, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 22, 22, 22, 22, 22, 1, 54, 54, 54, 54, 54, 54, 54, 24, 24, 3, 2, 2, 2, 1, 1, 23, 1, 1] 155 rigid atoms, others: [34, 35, 37, 38, 7, 8, 9, 10, 11, 12, 20] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36]) total number of confs: 214 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074066 none CC1CC1CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 155 conformations in input total number of sets (complete confs): 155 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 8, 38, 38, 38, 54, 54, 54, 54, 124, 124, 155, 155, 155, 155, 155, 54, 2, 2, 2, 1, 1, 1, 1, 8, 8, 38, 54, 54, 54, 54, 54, 155, 54, 54] 155 rigid atoms, others: [0, 1, 2, 3, 4, 24, 25, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 436 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074066 none CC1CC1CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 155 conformations in input total number of sets (complete confs): 155 using faster count positions algorithm for large data unique positions, atoms: [155, 155, 155, 125, 29, 29, 29, 23, 23, 23, 22, 10, 1, 10, 1, 1, 1, 1, 1, 1, 23, 155, 155, 155, 155, 155, 155, 155, 125, 125, 29, 23, 23, 23, 22, 23, 1, 23, 23] 155 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: 531 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074066 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074066 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074066/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074066 Building REAL250005074067 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074067' /scratch/stefan/7916156/working/building/REAL250005074067 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074067 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074067/0 /scratch/stefan/7916156/working/building/REAL250005074067 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 175) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/175 `/scratch/stefan/7916156/working/3D/175' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(C)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074067.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074067/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074067 none CC(C)C(C)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 46, 50, 19, 46, 19, 19, 17, 17, 17, 16, 7, 1, 7, 1, 1, 1, 1, 1, 1, 17, 50, 50, 50, 50, 50, 50, 50, 46, 46, 46, 46, 19, 17, 17, 17, 17, 16, 1, 17, 17] 50 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: 178 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074067 none CC(C)C(C)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 14, 19, 3, 14, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 16, 16, 16, 16, 16, 1, 20, 20, 20, 20, 20, 20, 20, 14, 14, 14, 14, 3, 2, 2, 2, 1, 1, 17, 1, 1] 50 rigid atoms, others: [36, 37, 7, 8, 9, 10, 11, 12, 40, 20, 39] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074067 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074067 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074067/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074067 Building REAL250005074068 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074068' /scratch/stefan/7916156/working/building/REAL250005074068 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074068 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074068/0 /scratch/stefan/7916156/working/building/REAL250005074068 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 176) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/176 `/scratch/stefan/7916156/working/3D/176' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1C[C@H]1C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074068.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074068/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074068 none CC[C@@H]1C[C@H]1C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 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', '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, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 124 conformations in input total number of sets (complete confs): 124 using faster count positions algorithm for large data unique positions, atoms: [37, 23, 23, 23, 23, 3, 23, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 22, 22, 22, 22, 23, 1, 37, 37, 37, 37, 37, 23, 23, 3, 2, 2, 2, 1, 1, 23, 1, 1] 124 rigid atoms, others: [34, 35, 37, 38, 9, 10, 11, 12, 13, 14, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36]) total number of confs: 178 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074068 none CC[C@@H]1C[C@H]1C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 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', '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, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [3, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 23, 23, 23, 23, 77, 77, 111, 111, 111, 111, 111, 23, 3, 3, 3, 3, 3, 1, 1, 13, 23, 23, 23, 23, 23, 111, 23, 23] 124 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 28, 29] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38]) 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.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: REAL250005074068 none CC[C@@H]1C[C@H]1C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 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', '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, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 111, 111, 111, 111, 31, 111, 31, 31, 23, 23, 23, 23, 9, 1, 9, 1, 1, 1, 1, 1, 1, 23, 124, 124, 124, 124, 124, 111, 111, 31, 23, 23, 23, 22, 23, 1, 23, 23] 124 rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 349 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074068 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074068 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074068/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074068 Building REAL250005074069 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074069' /scratch/stefan/7916156/working/building/REAL250005074069 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074069 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074069/0 /scratch/stefan/7916156/working/building/REAL250005074069 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 177) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/177 `/scratch/stefan/7916156/working/3D/177' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2CC23CC3)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074069.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074069/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074069 none CC1(NC(=O)C2CC23CC3)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 1, 11, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [24, 13, 13, 1, 13, 1, 1, 1, 1, 1, 24, 24, 24, 76, 76, 99, 99, 99, 99, 99, 24, 24, 24, 24, 13, 1, 1, 1, 1, 1, 1, 1, 24, 24, 99, 24, 24] 99 rigid atoms, others: [3, 5, 6, 7, 8, 9, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36]) total number of confs: 260 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074069 none CC1(NC(=O)C2CC23CC3)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 1, 11, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 3, 3, 3, 24, 24, 24, 24, 1, 1, 1, 6, 6, 20, 20, 20, 20, 20, 1, 2, 2, 2, 3, 24, 24, 24, 24, 24, 24, 24, 1, 1, 20, 1, 1] 99 rigid atoms, others: [0, 1, 2, 35, 36, 33, 32, 10, 11, 12, 20] set([3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34]) total number of confs: 91 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.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: REAL250005074069 none CC1(NC(=O)C2CC23CC3)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 1, 11, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 20, 31, 31, 31, 99, 99, 99, 99, 20, 8, 1, 8, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 31, 99, 99, 99, 99, 99, 99, 99, 20, 20, 1, 20, 20] 99 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: 255 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074069 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074069 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074069/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074069 Building REAL250005074070 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074070' /scratch/stefan/7916156/working/building/REAL250005074070 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074070 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074070/0 /scratch/stefan/7916156/working/building/REAL250005074070 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 178) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/178 `/scratch/stefan/7916156/working/3D/178' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)[C@@H]2CC(=O)N2)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074070.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074070/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074070 none CC1(NC(=O)[C@@H]2CC(=O)N2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', '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, 8, 1, 11, 5, 7, 5, 1, 11, 8, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 24, 24, 24, 70, 70, 85, 85, 85, 85, 85, 24, 24, 24, 24, 13, 1, 1, 1, 24, 24, 85, 24, 24] 85 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 26, 27, 28] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33]) total number of confs: 231 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074070 none CC1(NC(=O)[C@@H]2CC(=O)N2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', '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, 8, 1, 11, 5, 7, 5, 1, 11, 8, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 3, 3, 3, 24, 24, 24, 24, 24, 1, 1, 1, 6, 6, 22, 22, 22, 22, 22, 1, 2, 2, 2, 3, 24, 24, 24, 1, 1, 22, 1, 1] 85 rigid atoms, others: [0, 1, 2, 33, 32, 11, 12, 13, 21, 29, 30] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 31]) total number of confs: 93 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.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: REAL250005074070 none CC1(NC(=O)[C@@H]2CC(=O)N2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', '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, 8, 1, 11, 5, 7, 5, 1, 11, 8, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 36, 36, 36, 85, 85, 85, 85, 85, 22, 8, 1, 8, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 36, 85, 85, 85, 22, 22, 1, 22, 22] 85 rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33]) total number of confs: 236 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074070 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074070 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074070/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074070 Building REAL250005074071 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074071' /scratch/stefan/7916156/working/building/REAL250005074071 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074071 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074071/0 /scratch/stefan/7916156/working/building/REAL250005074071 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 179) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/179 `/scratch/stefan/7916156/working/3D/179' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)[C@H]2CC(=O)N2)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074071.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074071/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074071 none CC1(NC(=O)[C@H]2CC(=O)N2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', '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, 8, 1, 11, 5, 7, 5, 1, 11, 8, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [23, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 23, 23, 23, 57, 57, 66, 66, 66, 66, 66, 23, 23, 23, 23, 13, 1, 1, 1, 23, 23, 66, 23, 23] 66 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 26, 27, 28] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33]) total number of confs: 189 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074071 none CC1(NC(=O)[C@H]2CC(=O)N2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', '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, 8, 1, 11, 5, 7, 5, 1, 11, 8, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 3, 3, 3, 23, 23, 23, 23, 23, 1, 1, 1, 6, 6, 17, 17, 17, 17, 17, 1, 2, 2, 2, 3, 23, 23, 23, 1, 1, 17, 1, 1] 66 rigid atoms, others: [0, 1, 2, 33, 32, 11, 12, 13, 21, 29, 30] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 31]) 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.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: REAL250005074071 none CC1(NC(=O)[C@H]2CC(=O)N2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', '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, 8, 1, 11, 5, 7, 5, 1, 11, 8, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [18, 18, 18, 25, 25, 25, 66, 66, 66, 66, 66, 17, 7, 1, 7, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 25, 66, 66, 66, 17, 17, 1, 18, 18] 66 rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33]) total number of confs: 178 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074071 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074071 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074071/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074071 Building REAL250005074072 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074072' /scratch/stefan/7916156/working/building/REAL250005074072 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074072 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074072/0 /scratch/stefan/7916156/working/building/REAL250005074072 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 180) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/180 `/scratch/stefan/7916156/working/3D/180' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2CSC2)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074072.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074072/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074072 none CC1(NC(=O)C2CSC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 8, 1, 11, 5, 5, 14, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [20, 11, 11, 1, 11, 1, 1, 1, 1, 20, 20, 20, 56, 56, 63, 63, 63, 63, 63, 20, 20, 20, 20, 11, 1, 1, 1, 1, 1, 20, 20, 63, 20, 20] 63 rigid atoms, others: [3, 5, 6, 7, 8, 24, 25, 26, 27, 28] set([0, 1, 2, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33]) total number of confs: 177 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074072 none CC1(NC(=O)C2CSC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 8, 1, 11, 5, 5, 14, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 3, 3, 3, 20, 20, 20, 1, 1, 1, 6, 6, 21, 21, 21, 21, 21, 1, 2, 2, 2, 3, 20, 20, 20, 20, 20, 1, 1, 21, 1, 1] 63 rigid atoms, others: [0, 1, 2, 33, 32, 9, 10, 11, 19, 29, 30] set([3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074072 none CC1(NC(=O)C2CSC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 8, 1, 11, 5, 5, 14, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [21, 21, 21, 32, 32, 32, 63, 63, 63, 21, 10, 1, 10, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 32, 63, 63, 63, 63, 63, 21, 21, 1, 21, 21] 63 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33]) total number of confs: 185 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074072 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074072 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074072/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074072 Building REAL250005074073 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074073' /scratch/stefan/7916156/working/building/REAL250005074073 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074073 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074073/0 /scratch/stefan/7916156/working/building/REAL250005074073 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 181) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/181 `/scratch/stefan/7916156/working/3D/181' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074073.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074073/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074073 none C=CCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 21, 21, 21, 16, 16, 16, 16, 8, 1, 8, 1, 1, 1, 1, 1, 1, 16, 56, 56, 56, 56, 56, 21, 16, 16, 16, 16, 16, 1, 16, 16] 56 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: 193 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074073 none C=CCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [32, 19, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 16, 16, 16, 16, 16, 1, 32, 32, 32, 19, 19, 3, 2, 2, 2, 1, 1, 16, 1, 1] 56 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 18, 28, 29, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074073 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074073 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074073/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074073 Building REAL250005074074 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074074' /scratch/stefan/7916156/working/building/REAL250005074074 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005074074 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074074/0 /scratch/stefan/7916156/working/building/REAL250005074074 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 182) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/182 `/scratch/stefan/7916156/working/3D/182' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074074.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074074/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074074 none C[NH+](C)CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 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, 8, 10, 10, 8, 8, 8, 7, 7, 7, 7, 5, 1, 5, 1, 1, 1, 1, 1, 1, 7, 10, 10, 10, 10, 10, 10, 8, 8, 8, 7, 7, 7, 7, 7, 1, 7, 7] 10 rigid atoms, others: [35, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37]) total number of confs: 30 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074074 none C[NH+](C)CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 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: [7, 5, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 5, 5, 3, 2, 2, 2, 1, 1, 7, 1, 1] 10 rigid atoms, others: [33, 34, 36, 37, 7, 8, 9, 10, 11, 12, 20] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074074 /scratch/stefan/7916156/working /scratch/stefan/7916156 mkdir: created directory `1' /scratch/stefan/7916156/working/building/REAL250005074074/1 /scratch/stefan/7916156/working/building/REAL250005074074 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 1 (index: 183) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/183 `/scratch/stefan/7916156/working/3D/183' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074074.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005074074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074074/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074074 none CN(C)CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [52, 49, 52, 24, 24, 24, 22, 22, 22, 21, 9, 1, 9, 1, 1, 1, 1, 1, 1, 22, 52, 52, 52, 52, 52, 52, 49, 49, 24, 22, 22, 22, 22, 21, 1, 22, 22] 52 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]) total number of confs: 175 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074074 none CN(C)CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [18, 14, 18, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 21, 21, 21, 21, 21, 1, 18, 18, 18, 18, 18, 18, 14, 14, 3, 2, 2, 2, 1, 1, 22, 1, 1] 52 rigid atoms, others: [32, 33, 35, 36, 6, 7, 8, 9, 10, 11, 19] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074074 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074074 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 1: /scratch/stefan/7916156/working/building/REAL250005074074/1.* 0: /scratch/stefan/7916156/working/building/REAL250005074074/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074074 Building REAL250005074075 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074075' /scratch/stefan/7916156/working/building/REAL250005074075 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074075 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074075/0 /scratch/stefan/7916156/working/building/REAL250005074075 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 184) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/184 `/scratch/stefan/7916156/working/3D/184' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(O)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074075.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074075/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074075 none C=CC(O)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 23, 50, 23, 23, 19, 19, 19, 18, 9, 1, 9, 1, 1, 1, 1, 1, 1, 19, 50, 50, 50, 50, 150, 23, 19, 19, 19, 18, 19, 1, 19, 19] 150 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33]) total number of confs: 319 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074075 none C=CC(O)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [25, 17, 3, 17, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 18, 18, 18, 18, 18, 1, 25, 25, 25, 17, 51, 3, 2, 2, 2, 1, 1, 19, 1, 1] 150 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 19, 29, 30] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074075 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074075 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074075/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074075 Building REAL250005074076 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074076' /scratch/stefan/7916156/working/building/REAL250005074076 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074076 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074076/0 /scratch/stefan/7916156/working/building/REAL250005074076 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 185) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/185 `/scratch/stefan/7916156/working/3D/185' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2COC2)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074076.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074076/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074076 none CC1(NC(=O)C2COC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [20, 11, 11, 1, 11, 1, 1, 1, 1, 20, 20, 20, 61, 61, 65, 65, 65, 65, 65, 20, 20, 20, 20, 11, 1, 1, 1, 1, 1, 20, 20, 65, 20, 20] 65 rigid atoms, others: [3, 5, 6, 7, 8, 24, 25, 26, 27, 28] set([0, 1, 2, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33]) total number of confs: 185 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074076 none CC1(NC(=O)C2COC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 3, 3, 3, 20, 20, 20, 1, 1, 1, 6, 6, 20, 20, 20, 20, 20, 1, 2, 2, 2, 3, 20, 20, 20, 20, 20, 1, 1, 20, 1, 1] 65 rigid atoms, others: [0, 1, 2, 33, 32, 9, 10, 11, 19, 29, 30] set([3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31]) 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.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: REAL250005074076 none CC1(NC(=O)C2COC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [20, 20, 20, 30, 30, 30, 65, 65, 65, 20, 9, 1, 9, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 30, 65, 65, 65, 65, 65, 20, 20, 1, 20, 20] 65 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33]) total number of confs: 191 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074076 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074076 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074076/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074076 Building REAL250005074077 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074077' /scratch/stefan/7916156/working/building/REAL250005074077 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074077 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074077/0 /scratch/stefan/7916156/working/building/REAL250005074077 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 186) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/186 `/scratch/stefan/7916156/working/3D/186' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](C)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074077.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074077/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074077 none CO[C@H](C)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 1, 11, 8, 5, 5, 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, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [37, 36, 20, 36, 36, 20, 20, 18, 18, 18, 18, 9, 1, 9, 1, 1, 1, 1, 1, 1, 18, 37, 37, 37, 36, 36, 36, 20, 18, 18, 18, 18, 18, 1, 18, 18] 37 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: 115 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074077 none CO[C@H](C)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 1, 11, 8, 5, 5, 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, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [19, 16, 3, 16, 16, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 18, 18, 18, 18, 18, 1, 19, 19, 19, 16, 16, 16, 3, 2, 2, 2, 1, 1, 18, 1, 1] 37 rigid atoms, others: [32, 34, 35, 7, 8, 9, 10, 11, 12, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074077 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074077 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074077/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074077 Building REAL250005074078 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074078' /scratch/stefan/7916156/working/building/REAL250005074078 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074078 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074078/0 /scratch/stefan/7916156/working/building/REAL250005074078 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 187) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/187 `/scratch/stefan/7916156/working/3D/187' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC(O)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074078.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074078/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074078 none CC=CC(O)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 234 conformations in input total number of sets (complete confs): 234 using faster count positions algorithm for large data unique positions, atoms: [78, 78, 62, 28, 62, 28, 28, 23, 23, 23, 22, 9, 1, 9, 1, 1, 1, 1, 1, 1, 23, 78, 78, 78, 78, 78, 62, 186, 28, 23, 23, 23, 22, 23, 1, 23, 23] 234 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: 456 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074078 none CC=CC(O)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [46, 46, 21, 3, 21, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 22, 22, 22, 22, 22, 1, 46, 46, 46, 46, 46, 21, 63, 3, 2, 2, 2, 1, 1, 23, 1, 1] 234 rigid atoms, others: [32, 33, 35, 36, 7, 8, 9, 10, 11, 12, 20] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34]) total number of confs: 248 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074078 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074078 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074078/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074078 Building REAL250005074079 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074079' /scratch/stefan/7916156/working/building/REAL250005074079 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005074079 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074079/0 /scratch/stefan/7916156/working/building/REAL250005074079 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 188) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/188 `/scratch/stefan/7916156/working/3D/188' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1)[NH+](C)C) `REAL250005074079.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074079/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074079 none C[C@@H](C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1)[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', '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, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 9, 6, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [22, 14, 22, 14, 14, 12, 12, 12, 12, 5, 1, 5, 1, 1, 1, 1, 1, 1, 12, 22, 22, 22, 22, 22, 22, 22, 14, 12, 12, 12, 11, 12, 1, 12, 12, 22, 22, 22, 22, 22, 22] 22 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, 39, 40]) total number of confs: 66 number of broken/clashed sets: 15 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074079 none C[C@@H](C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1)[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', '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, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 9, 6, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [11, 3, 11, 3, 3, 1, 1, 1, 1, 1, 1, 4, 4, 11, 11, 11, 11, 12, 1, 11, 16, 16, 16, 11, 11, 11, 3, 2, 2, 2, 1, 1, 12, 1, 1, 16, 16, 16, 16, 16, 16] 22 rigid atoms, others: [33, 34, 5, 6, 7, 8, 9, 10, 18, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 35, 36, 37, 38, 39, 40]) total number of confs: 92 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074079 /scratch/stefan/7916156/working /scratch/stefan/7916156 mkdir: created directory `1' /scratch/stefan/7916156/working/building/REAL250005074079/1 /scratch/stefan/7916156/working/building/REAL250005074079 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 1 (index: 189) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/189 `/scratch/stefan/7916156/working/3D/189' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1)N(C)C) `REAL250005074079.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005074079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074079/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074079 none C[C@@H](C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', '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, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 10, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 16, 31, 16, 16, 14, 14, 14, 14, 7, 1, 7, 1, 1, 1, 1, 1, 1, 14, 31, 31, 31, 31, 31, 31, 16, 14, 14, 14, 14, 14, 1, 14, 14, 31, 31, 31, 31, 31, 31] 31 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 90 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074079 none C[C@@H](C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', '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, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 10, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [12, 3, 12, 3, 3, 1, 1, 1, 1, 1, 1, 7, 7, 14, 14, 14, 14, 14, 1, 12, 12, 12, 12, 12, 12, 3, 2, 2, 2, 1, 1, 14, 1, 1, 12, 12, 12, 12, 12, 12] 31 rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 18, 29, 30] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 34, 35, 36, 37, 38, 39]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074079 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074079 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 1: /scratch/stefan/7916156/working/building/REAL250005074079/1.* 0: /scratch/stefan/7916156/working/building/REAL250005074079/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074079 Building REAL250005074080 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074080' /scratch/stefan/7916156/working/building/REAL250005074080 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074080 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074080/0 /scratch/stefan/7916156/working/building/REAL250005074080 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 190) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/190 `/scratch/stefan/7916156/working/3D/190' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC=C(F)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074080.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074080/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074080 none CCC=C(F)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 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', 'C.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, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [86, 54, 54, 20, 54, 20, 20, 14, 14, 14, 13, 6, 1, 6, 1, 1, 1, 1, 1, 1, 14, 86, 86, 86, 86, 86, 54, 20, 14, 14, 14, 14, 13, 1, 14, 14] 86 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: 337 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074080 none CCC=C(F)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 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', 'C.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, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [30, 15, 15, 3, 15, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 13, 13, 13, 13, 13, 1, 30, 30, 30, 30, 30, 15, 3, 2, 2, 2, 1, 1, 14, 1, 1] 86 rigid atoms, others: [32, 34, 35, 7, 8, 9, 10, 11, 12, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074080 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074080 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074080/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074080 Building REAL250005074081 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074081' /scratch/stefan/7916156/working/building/REAL250005074081 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074081 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074081/0 /scratch/stefan/7916156/working/building/REAL250005074081 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 191) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/191 `/scratch/stefan/7916156/working/3D/191' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC=CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074081.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074081.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074081/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074081 none CCC=CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [96, 75, 75, 34, 34, 34, 25, 25, 25, 24, 9, 1, 9, 1, 1, 1, 1, 1, 1, 25, 96, 96, 96, 96, 96, 75, 75, 34, 25, 25, 25, 25, 24, 1, 25, 25] 96 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: 343 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074081 none CCC=CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [36, 21, 21, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 24, 24, 24, 24, 24, 1, 36, 36, 36, 36, 36, 21, 21, 3, 2, 2, 2, 1, 1, 25, 1, 1] 96 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074081 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074081 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074081/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074081 Building REAL250005074082 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074082' /scratch/stefan/7916156/working/building/REAL250005074082 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types Protomer extracton resulted in 0 protomers Marking REAL250005074082 as failed and skipping /scratch/stefan/7916156/working /scratch/stefan/7916156 `/scratch/stefan/7916156/working/building/REAL250005074082' -> `/scratch/stefan/7916156/failed/REAL250005074082' Building REAL250005074083 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074083' /scratch/stefan/7916156/working/building/REAL250005074083 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074083 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074083/0 /scratch/stefan/7916156/working/building/REAL250005074083 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 192) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/192 `/scratch/stefan/7916156/working/3D/192' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)CO)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074083.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074083/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074083 none CC1(NC(=O)CO)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', '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, 8, 1, 11, 5, 12, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 23, 37, 37, 37, 43, 23, 10, 1, 10, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 37, 43, 43, 129, 23, 23, 1, 23, 23] 129 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29]) total number of confs: 260 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074083 none CC1(NC(=O)CO)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', '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, 8, 1, 11, 5, 12, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 3, 3, 3, 15, 1, 1, 1, 6, 6, 23, 23, 23, 23, 23, 1, 2, 2, 2, 3, 15, 15, 45, 1, 1, 23, 1, 1] 129 rigid atoms, others: [0, 1, 2, 7, 8, 9, 17, 25, 26, 28, 29] set([3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 27]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074083 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074083 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074083/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074083 Building REAL250005074084 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074084' /scratch/stefan/7916156/working/building/REAL250005074084 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074084 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074084/0 /scratch/stefan/7916156/working/building/REAL250005074084 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 193) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/193 `/scratch/stefan/7916156/working/3D/193' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C=CC(N)=O)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074084.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074084/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074084 none CC1(NC(=O)C=CC(N)=O)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 8, 11, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 4, 6, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 22, 22, 35, 35, 35, 73, 73, 85, 87, 21, 9, 1, 9, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 35, 73, 73, 87, 85, 22, 21, 1, 22, 22] 87 rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33]) total number of confs: 260 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074084 none CC1(NC(=O)C=CC(N)=O)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 8, 11, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 4, 6, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 3, 3, 3, 23, 23, 44, 46, 1, 1, 1, 6, 6, 21, 21, 21, 21, 21, 1, 2, 2, 2, 3, 23, 23, 46, 44, 1, 1, 22, 1, 1] 87 rigid atoms, others: [0, 1, 2, 33, 32, 10, 11, 12, 20, 29, 30] set([3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 31]) total number of confs: 160 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074084 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074084 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074084/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074084 Building REAL250005074085 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074085' /scratch/stefan/7916156/working/building/REAL250005074085 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074085 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074085/0 /scratch/stefan/7916156/working/building/REAL250005074085 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 194) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/194 `/scratch/stefan/7916156/working/3D/194' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074085.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074085/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074085 none CC(O)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [36, 25, 36, 25, 25, 20, 20, 20, 20, 8, 1, 8, 1, 1, 1, 1, 1, 1, 20, 36, 36, 36, 36, 108, 25, 20, 20, 20, 20, 20, 1, 20, 20] 108 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: 220 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074085 none CC(O)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [17, 3, 17, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 20, 20, 20, 20, 20, 1, 17, 17, 17, 17, 51, 3, 2, 2, 2, 1, 1, 20, 1, 1] 108 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 18, 28, 29, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074085 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074085 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074085/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074085 Building REAL250005074086 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074086' /scratch/stefan/7916156/working/building/REAL250005074086 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074086 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074086/0 /scratch/stefan/7916156/working/building/REAL250005074086 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 195) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/195 `/scratch/stefan/7916156/working/3D/195' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C(O)C2CC2)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074086.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074086/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074086 none CC1(NC(=O)C(O)C2CC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 315 conformations in input total number of sets (complete confs): 315 using faster count positions algorithm for large data unique positions, atoms: [50, 33, 33, 9, 33, 1, 9, 1, 1, 1, 50, 50, 50, 95, 95, 105, 105, 105, 105, 105, 50, 50, 50, 50, 33, 9, 27, 1, 1, 1, 1, 1, 50, 50, 105, 50, 50] 315 rigid atoms, others: [5, 7, 8, 9, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 32, 33, 34, 35, 36]) total number of confs: 337 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074086 none CC1(NC(=O)C(O)C2CC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 315 conformations in input total number of sets (complete confs): 315 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 3, 3, 3, 21, 21, 50, 50, 1, 1, 1, 6, 6, 24, 24, 24, 24, 24, 1, 2, 2, 2, 3, 21, 63, 50, 50, 50, 50, 50, 1, 1, 24, 1, 1] 315 rigid atoms, others: [0, 1, 2, 35, 36, 33, 32, 10, 11, 12, 20] set([3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34]) total number of confs: 262 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074086 none CC1(NC(=O)C(O)C2CC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 315 conformations in input total number of sets (complete confs): 315 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 24, 36, 36, 36, 83, 83, 105, 105, 24, 10, 1, 10, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 36, 83, 249, 105, 105, 105, 105, 105, 24, 24, 1, 24, 24] 315 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: 625 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074086 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074086 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074086/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074086 Building REAL250005074087 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074087' /scratch/stefan/7916156/working/building/REAL250005074087 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074087 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074087/0 /scratch/stefan/7916156/working/building/REAL250005074087 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 196) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/196 `/scratch/stefan/7916156/working/3D/196' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(C)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074087.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074087/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074087 none C=CCC(C)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 171 conformations in input total number of sets (complete confs): 171 using faster count positions algorithm for large data unique positions, atoms: [171, 171, 117, 26, 117, 26, 26, 20, 20, 20, 19, 7, 1, 7, 1, 1, 1, 1, 1, 1, 20, 171, 171, 171, 171, 171, 117, 117, 117, 117, 26, 20, 20, 20, 20, 19, 1, 20, 20] 171 rigid atoms, others: [36, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 687 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074087 none C=CCC(C)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 171 conformations in input total number of sets (complete confs): 171 using faster count positions algorithm for large data unique positions, atoms: [104, 72, 23, 3, 23, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 19, 19, 19, 19, 19, 1, 104, 104, 104, 72, 72, 23, 23, 23, 23, 3, 2, 2, 2, 1, 1, 20, 1, 1] 171 rigid atoms, others: [34, 35, 37, 38, 7, 8, 9, 10, 11, 12, 20] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36]) total number of confs: 430 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074087 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074087 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074087/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074087 Building REAL250005074088 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074088' /scratch/stefan/7916156/working/building/REAL250005074088 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074088 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074088/0 /scratch/stefan/7916156/working/building/REAL250005074088 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 197) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/197 `/scratch/stefan/7916156/working/3D/197' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2CC2F)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074088.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074088.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074088/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074088 none CC1(NC(=O)C2CC2F)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 15, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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: [23, 12, 12, 1, 12, 1, 1, 1, 1, 23, 23, 23, 69, 69, 81, 81, 81, 81, 81, 23, 23, 23, 23, 12, 1, 1, 1, 1, 23, 23, 81, 23, 23] 81 rigid atoms, others: [3, 5, 6, 7, 8, 24, 25, 26, 27] set([0, 1, 2, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32]) total number of confs: 224 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074088 none CC1(NC(=O)C2CC2F)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 15, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 3, 3, 3, 23, 23, 23, 1, 1, 1, 6, 6, 23, 23, 23, 23, 23, 1, 2, 2, 2, 3, 23, 23, 23, 23, 1, 1, 23, 1, 1] 81 rigid atoms, others: [0, 1, 2, 32, 9, 10, 11, 19, 28, 29, 31] set([3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 30]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074088 none CC1(NC(=O)C2CC2F)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 15, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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: [23, 23, 23, 37, 37, 37, 81, 81, 81, 23, 10, 1, 10, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 37, 81, 81, 81, 81, 23, 23, 1, 23, 23] 81 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32]) total number of confs: 237 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074088 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074088 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074088/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074088 Building REAL250005074089 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074089' /scratch/stefan/7916156/working/building/REAL250005074089 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005074089 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074089/0 /scratch/stefan/7916156/working/building/REAL250005074089 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 198) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/198 `/scratch/stefan/7916156/working/3D/198' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1)[NH+](C)C) `REAL250005074089.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074089.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074089/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074089 none C[C@@H](C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1)[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', '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, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 9, 6, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [22, 14, 22, 14, 14, 12, 12, 12, 12, 5, 1, 5, 1, 1, 1, 1, 1, 1, 12, 22, 22, 22, 22, 22, 22, 22, 14, 12, 12, 12, 11, 12, 1, 12, 12, 22, 22, 22, 22, 22, 22] 22 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, 39, 40]) total number of confs: 66 number of broken/clashed sets: 15 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074089 none C[C@@H](C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1)[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', '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, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 9, 6, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [11, 3, 11, 3, 3, 1, 1, 1, 1, 1, 1, 4, 4, 11, 11, 11, 11, 12, 1, 11, 16, 16, 16, 11, 11, 11, 3, 2, 2, 2, 1, 1, 12, 1, 1, 16, 16, 16, 16, 16, 16] 22 rigid atoms, others: [33, 34, 5, 6, 7, 8, 9, 10, 18, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 35, 36, 37, 38, 39, 40]) total number of confs: 92 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074089 /scratch/stefan/7916156/working /scratch/stefan/7916156 mkdir: created directory `1' /scratch/stefan/7916156/working/building/REAL250005074089/1 /scratch/stefan/7916156/working/building/REAL250005074089 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 1 (index: 199) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/199 `/scratch/stefan/7916156/working/3D/199' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1)N(C)C) `REAL250005074089.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005074089.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074089/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074089 none C[C@@H](C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', '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, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 10, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 16, 31, 16, 16, 14, 14, 14, 14, 7, 1, 7, 1, 1, 1, 1, 1, 1, 14, 31, 31, 31, 31, 31, 31, 16, 14, 14, 14, 14, 14, 1, 14, 14, 31, 31, 31, 31, 31, 31] 31 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 90 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074089 none C[C@@H](C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', '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, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 10, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [12, 3, 12, 3, 3, 1, 1, 1, 1, 1, 1, 7, 7, 14, 14, 14, 14, 14, 1, 12, 12, 12, 12, 12, 12, 3, 2, 2, 2, 1, 1, 14, 1, 1, 12, 12, 12, 12, 12, 12] 31 rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 18, 29, 30] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 34, 35, 36, 37, 38, 39]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074089 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074089 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 1: /scratch/stefan/7916156/working/building/REAL250005074089/1.* 0: /scratch/stefan/7916156/working/building/REAL250005074089/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074089 Building REAL250005074090 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074090' /scratch/stefan/7916156/working/building/REAL250005074090 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074090 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074090/0 /scratch/stefan/7916156/working/building/REAL250005074090 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 200) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/200 `/scratch/stefan/7916156/working/3D/200' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)CCF)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074090.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074090/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074090 none CC1(NC(=O)CCF)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 15, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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: [25, 25, 25, 41, 41, 41, 108, 108, 24, 8, 1, 8, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 41, 108, 108, 108, 108, 25, 24, 1, 25, 25] 108 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]) total number of confs: 388 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074090 none CC1(NC(=O)CCF)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 15, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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: [1, 1, 1, 3, 3, 3, 19, 42, 1, 1, 1, 6, 6, 24, 24, 24, 24, 24, 1, 2, 2, 2, 3, 19, 19, 42, 42, 1, 1, 25, 1, 1] 108 rigid atoms, others: [0, 1, 2, 8, 9, 10, 18, 27, 28, 30, 31] set([3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 29]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074090 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074090 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074090/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074090 Building REAL250005074091 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074091' /scratch/stefan/7916156/working/building/REAL250005074091 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074091 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074091/0 /scratch/stefan/7916156/working/building/REAL250005074091 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 201) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/201 `/scratch/stefan/7916156/working/3D/201' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1)=C1CC1) `REAL250005074091.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074091.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074091/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074091 none CC(C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1)=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.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, 5, 1, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 21, 21, 21, 15, 15, 15, 15, 7, 1, 7, 1, 1, 1, 1, 1, 1, 15, 59, 59, 59, 59, 59, 59, 21, 15, 15, 15, 15, 15, 1, 15, 15, 59, 59, 59, 59] 59 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36]) total number of confs: 148 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074091 none CC(C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1)=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.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, 5, 1, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [22, 2, 2, 2, 1, 1, 1, 1, 1, 1, 6, 6, 15, 15, 15, 15, 15, 1, 22, 22, 22, 22, 22, 22, 2, 2, 2, 2, 1, 1, 15, 1, 1, 22, 22, 22, 22] 59 rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 17, 28, 29, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 33, 34, 35, 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.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: REAL250005074091 none CC(C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1)=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.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, 5, 1, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 13, 13, 13, 22, 22, 22, 22, 49, 49, 59, 59, 59, 59, 59, 22, 1, 1, 1, 2, 2, 2, 13, 22, 22, 22, 22, 22, 59, 22, 22, 1, 1, 1, 1] 59 rigid atoms, others: [0, 1, 2, 35, 36, 33, 34, 18, 19, 20] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 174 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074091 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074091 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074091/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074091 Building REAL250005074092 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074092' /scratch/stefan/7916156/working/building/REAL250005074092 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074092 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074092/0 /scratch/stefan/7916156/working/building/REAL250005074092 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 202) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/202 `/scratch/stefan/7916156/working/3D/202' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1CC1C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074092.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074092/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074092 none CCC1CC1C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [18, 17, 17, 17, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 23, 23, 23, 23, 23, 1, 18, 18, 18, 18, 18, 17, 17, 17, 17, 3, 2, 2, 2, 1, 1, 23, 1, 1] 60 rigid atoms, others: [34, 35, 37, 38, 7, 8, 9, 10, 11, 12, 20] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36]) total number of confs: 84 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074092 none CCC1CC1C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 9, 9, 9, 17, 17, 17, 17, 48, 48, 60, 60, 60, 60, 60, 17, 3, 3, 3, 3, 3, 1, 1, 1, 1, 9, 17, 17, 17, 17, 17, 60, 17, 17] 60 rigid atoms, others: [1, 2, 3, 4, 5, 26, 27, 28, 29] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074092 none CCC1CC1C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [60, 60, 60, 60, 30, 30, 30, 23, 23, 23, 23, 10, 1, 10, 1, 1, 1, 1, 1, 1, 23, 60, 60, 60, 60, 60, 60, 60, 60, 60, 30, 23, 23, 23, 23, 23, 1, 23, 23] 60 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: 157 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074092 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074092 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074092/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074092 Building REAL250005074093 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074093' /scratch/stefan/7916156/working/building/REAL250005074093 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074093 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074093/0 /scratch/stefan/7916156/working/building/REAL250005074093 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 203) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/203 `/scratch/stefan/7916156/working/3D/203' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)CC2(O)CC2)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074093.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074093.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074093/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074093 none CC1(NC(=O)CC2(O)CC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 327 conformations in input total number of sets (complete confs): 327 using faster count positions algorithm for large data unique positions, atoms: [54, 38, 38, 9, 38, 1, 1, 1, 1, 1, 54, 54, 54, 100, 100, 109, 109, 109, 109, 109, 54, 54, 54, 54, 38, 9, 9, 6, 1, 1, 1, 1, 54, 54, 109, 54, 54] 327 rigid atoms, others: [5, 6, 7, 8, 9, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36]) total number of confs: 334 number of broken/clashed sets: 14 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074093 none CC1(NC(=O)CC2(O)CC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 327 conformations in input total number of sets (complete confs): 327 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 3, 3, 3, 25, 54, 54, 54, 1, 1, 1, 6, 6, 22, 22, 22, 22, 22, 1, 2, 2, 2, 3, 25, 25, 162, 54, 54, 54, 54, 1, 1, 22, 1, 1] 327 rigid atoms, others: [0, 1, 2, 35, 36, 33, 32, 10, 11, 12, 20] set([3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34]) total number of confs: 377 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.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: REAL250005074093 none CC1(NC(=O)CC2(O)CC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 327 conformations in input total number of sets (complete confs): 327 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 34, 34, 34, 101, 109, 109, 109, 22, 8, 1, 8, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 34, 101, 101, 327, 109, 109, 109, 109, 22, 22, 1, 22, 22] 327 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: 699 number of broken/clashed sets: 14 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074093 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074093 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074093/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074093 Building REAL250005074094 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074094' /scratch/stefan/7916156/working/building/REAL250005074094 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074094 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074094/0 /scratch/stefan/7916156/working/building/REAL250005074094 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 204) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/204 `/scratch/stefan/7916156/working/3D/204' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C=CCF)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074094.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074094/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074094 none CC1(NC(=O)C=CCF)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 5, 15, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 36, 36, 36, 68, 68, 79, 21, 9, 1, 9, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 36, 68, 68, 79, 79, 22, 21, 1, 22, 22] 79 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32]) total number of confs: 266 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074094 none CC1(NC(=O)C=CCF)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 5, 15, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 3, 3, 3, 17, 17, 43, 1, 1, 1, 6, 6, 21, 21, 21, 21, 21, 1, 2, 2, 2, 3, 17, 17, 43, 43, 1, 1, 22, 1, 1] 79 rigid atoms, others: [0, 1, 2, 32, 9, 10, 11, 19, 28, 29, 31] set([3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 30]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074094 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074094 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074094/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074094 Building REAL250005074095 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074095' /scratch/stefan/7916156/working/building/REAL250005074095 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074095 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074095/0 /scratch/stefan/7916156/working/building/REAL250005074095 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 205) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/205 `/scratch/stefan/7916156/working/3D/205' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074095.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074095/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074095 none C#CCCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [96, 96, 83, 30, 30, 30, 20, 20, 20, 19, 8, 1, 8, 1, 1, 1, 1, 1, 1, 20, 96, 96, 96, 83, 83, 30, 20, 20, 20, 20, 19, 1, 20, 20] 96 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33]) total number of confs: 374 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074095 none C#CCCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [40, 40, 19, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 19, 19, 19, 19, 19, 1, 40, 40, 40, 19, 19, 3, 2, 2, 2, 1, 1, 20, 1, 1] 96 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 19, 29, 30] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074095 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074095 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074095/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074095 Building REAL250005074096 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074096' /scratch/stefan/7916156/working/building/REAL250005074096 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005074096 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074096/0 /scratch/stefan/7916156/working/building/REAL250005074096 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 206) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/206 `/scratch/stefan/7916156/working/3D/206' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)CN2CCC2)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074096.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074096/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074096 none CC1(NC(=O)CN2CCC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [34, 22, 22, 6, 22, 1, 1, 1, 1, 1, 34, 34, 34, 74, 74, 93, 93, 93, 93, 93, 34, 34, 34, 34, 22, 6, 6, 1, 1, 1, 1, 1, 1, 34, 34, 93, 34, 34] 93 rigid atoms, others: [32, 5, 6, 7, 8, 9, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 33, 34, 35, 36, 37]) total number of confs: 268 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074096 none CC1(NC(=O)CN2CCC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 3, 3, 3, 18, 34, 34, 34, 1, 1, 1, 6, 6, 23, 23, 23, 23, 23, 1, 2, 2, 2, 3, 18, 18, 34, 34, 34, 34, 34, 34, 1, 1, 24, 1, 1] 93 rigid atoms, others: [0, 1, 2, 36, 37, 33, 10, 11, 12, 34, 20] set([3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.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: REAL250005074096 none CC1(NC(=O)CN2CCC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 24, 24, 36, 36, 36, 87, 93, 93, 93, 23, 9, 1, 9, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 36, 87, 87, 93, 93, 93, 93, 93, 93, 23, 24, 1, 24, 24] 93 rigid atoms, others: [35, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37]) total number of confs: 326 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074096 /scratch/stefan/7916156/working /scratch/stefan/7916156 mkdir: created directory `1' /scratch/stefan/7916156/working/building/REAL250005074096/1 /scratch/stefan/7916156/working/building/REAL250005074096 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 1 (index: 207) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/207 `/scratch/stefan/7916156/working/3D/207' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C[NH+]2CCC2)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074096.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005074096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074096/1/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074096 none CC1(NC(=O)C[NH+]2CCC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [8, 8, 8, 4, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 14, 14, 14, 14, 14, 14, 14, 8, 8, 8, 8, 8, 4, 4, 1, 1, 1, 1, 1, 1, 8, 8, 14, 8, 8] 14 rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 11, 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: 45 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074096 none CC1(NC(=O)C[NH+]2CCC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 3, 3, 3, 5, 8, 8, 8, 8, 1, 1, 1, 4, 4, 8, 8, 8, 8, 8, 1, 2, 2, 2, 3, 5, 5, 8, 8, 8, 8, 8, 8, 1, 1, 9, 1, 1] 14 rigid atoms, others: [0, 1, 2, 35, 37, 38, 11, 12, 34, 13, 21] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074096 none CC1(NC(=O)C[NH+]2CCC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 9, 9, 13, 13, 13, 14, 14, 14, 14, 14, 8, 3, 1, 3, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 13, 14, 14, 14, 14, 14, 14, 14, 14, 8, 9, 1, 9, 9] 14 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: 41 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074096 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074096 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 1: /scratch/stefan/7916156/working/building/REAL250005074096/1.* 0: /scratch/stefan/7916156/working/building/REAL250005074096/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074096 Building REAL250005074097 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074097' /scratch/stefan/7916156/working/building/REAL250005074097 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074097 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074097/0 /scratch/stefan/7916156/working/building/REAL250005074097 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 208) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/208 `/scratch/stefan/7916156/working/3D/208' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#C[C@H]1C[C@H]1C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074097.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074097/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074097 none C#C[C@H]1C[C@H]1C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 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', 'C.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, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [17, 17, 17, 17, 17, 3, 17, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 23, 23, 23, 23, 23, 1, 17, 17, 17, 3, 2, 2, 2, 1, 1, 23, 1, 1] 66 rigid atoms, others: [33, 34, 9, 10, 11, 12, 13, 14, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 32]) total number of confs: 79 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074097 none C#C[C@H]1C[C@H]1C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 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', 'C.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, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 17, 17, 17, 17, 53, 53, 66, 66, 66, 66, 66, 17, 1, 1, 1, 10, 17, 17, 17, 17, 17, 66, 17, 17] 66 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 23, 24, 25] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074097 none C#C[C@H]1C[C@H]1C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 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', 'C.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, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [66, 66, 66, 66, 66, 32, 66, 32, 32, 24, 24, 24, 23, 9, 1, 9, 1, 1, 1, 1, 1, 1, 24, 66, 66, 66, 32, 24, 24, 24, 23, 23, 1, 24, 24] 66 rigid atoms, others: [32, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34]) total number of confs: 180 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074097 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074097 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074097/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074097 Building REAL250005074098 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074098' /scratch/stefan/7916156/working/building/REAL250005074098 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074098 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074098/0 /scratch/stefan/7916156/working/building/REAL250005074098 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 209) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/209 `/scratch/stefan/7916156/working/3D/209' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2C3CCC32)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074098.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074098/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074098 none CC1(NC(=O)C2C3CCC32)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 1, 11, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [21, 12, 12, 1, 12, 1, 1, 1, 1, 1, 21, 21, 21, 65, 65, 78, 78, 78, 78, 78, 21, 21, 21, 21, 12, 1, 1, 1, 1, 1, 1, 1, 21, 21, 78, 21, 21] 78 rigid atoms, others: [3, 5, 6, 7, 8, 9, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36]) total number of confs: 206 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074098 none CC1(NC(=O)C2C3CCC32)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 1, 11, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 3, 21, 21, 21, 21, 1, 1, 1, 6, 6, 22, 22, 22, 22, 22, 1, 2, 2, 2, 3, 21, 21, 21, 21, 21, 21, 21, 1, 1, 23, 1, 1] 78 rigid atoms, others: [0, 1, 2, 35, 36, 33, 32, 10, 11, 12, 20] set([3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074098 none CC1(NC(=O)C2C3CCC32)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 1, 11, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 23, 35, 35, 35, 78, 78, 78, 78, 22, 9, 1, 9, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 35, 78, 78, 78, 78, 78, 78, 78, 23, 22, 1, 23, 23] 78 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: 218 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074098 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074098 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074098/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074098 Building REAL250005074099 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074099' /scratch/stefan/7916156/working/building/REAL250005074099 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074099 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074099/0 /scratch/stefan/7916156/working/building/REAL250005074099 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 210) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/210 `/scratch/stefan/7916156/working/3D/210' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C1CCC1C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074099.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074099.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074099/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074099 none C=C1CCC1C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 20, 20, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 17, 17, 17, 17, 17, 1, 20, 20, 20, 20, 20, 20, 20, 3, 2, 2, 2, 1, 1, 17, 1, 1] 69 rigid atoms, others: [32, 33, 35, 36, 7, 8, 9, 10, 11, 12, 20] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34]) total number of confs: 78 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074099 none C=C1CCC1C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 12, 12, 12, 20, 20, 20, 20, 55, 55, 69, 69, 69, 69, 69, 20, 1, 1, 1, 1, 1, 1, 1, 12, 20, 20, 20, 20, 20, 69, 20, 20] 69 rigid atoms, others: [0, 1, 2, 3, 4, 5, 21, 22, 23, 24, 25, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 184 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.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: REAL250005074099 none C=C1CCC1C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [69, 69, 69, 69, 26, 26, 26, 17, 17, 17, 17, 8, 1, 8, 1, 1, 1, 1, 1, 1, 17, 69, 69, 69, 69, 69, 69, 69, 26, 17, 17, 17, 17, 17, 1, 17, 17] 69 rigid atoms, others: [34, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36]) total number of confs: 185 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074099 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074099 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074099/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074099 Building REAL250005074100 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074100' /scratch/stefan/7916156/working/building/REAL250005074100 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074100 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074100/0 /scratch/stefan/7916156/working/building/REAL250005074100 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 211) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/211 `/scratch/stefan/7916156/working/3D/211' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C(C(=O)NC2(C)CN(C(=O)C3=CC(=O)[N-]O3)C2)[C@H]1C) `REAL250005074100.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074100/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074100 none C[C@H]1C(C(=O)NC2(C)CN(C(=O)C3=CC(=O)[N-]O3)C2)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [20, 20, 20, 2, 2, 2, 1, 1, 1, 1, 1, 1, 6, 6, 16, 16, 16, 16, 16, 1, 20, 20, 20, 20, 20, 20, 20, 2, 2, 2, 2, 1, 1, 16, 1, 1, 20, 20, 20] 72 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 36, 37, 38]) total number of confs: 78 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074100 none C[C@H]1C(C(=O)NC2(C)CN(C(=O)C3=CC(=O)[N-]O3)C2)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 12, 12, 12, 20, 20, 20, 20, 59, 59, 72, 72, 72, 72, 72, 20, 1, 1, 1, 2, 2, 2, 1, 12, 20, 20, 20, 20, 20, 72, 20, 20, 2, 2, 2] 72 rigid atoms, others: [0, 1, 2, 3, 4, 20, 21, 22, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 201 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.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: REAL250005074100 none C[C@H]1C(C(=O)NC2(C)CN(C(=O)C3=CC(=O)[N-]O3)C2)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [72, 72, 72, 23, 23, 23, 17, 17, 17, 17, 8, 1, 8, 1, 1, 1, 1, 1, 1, 16, 72, 72, 72, 72, 72, 72, 72, 23, 17, 17, 17, 17, 17, 1, 16, 16, 72, 72, 72] 72 rigid atoms, others: [33, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38]) total number of confs: 188 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074100 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074100 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074100/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074100 Building REAL250005074101 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074101' /scratch/stefan/7916156/working/building/REAL250005074101 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005074101 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074101/0 /scratch/stefan/7916156/working/building/REAL250005074101 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 212) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/212 `/scratch/stefan/7916156/working/3D/212' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1)[NH+](C)C) `REAL250005074101.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074101.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074101/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074101 none C[C@H](C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1)[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', '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, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 9, 6, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [26, 15, 26, 15, 15, 13, 13, 13, 13, 8, 1, 8, 1, 1, 1, 1, 1, 1, 13, 26, 26, 26, 26, 26, 26, 26, 15, 13, 13, 13, 13, 13, 1, 13, 13, 26, 26, 26, 26, 26, 26] 26 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, 39, 40]) total number of confs: 84 number of broken/clashed sets: 18 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074101 none C[C@H](C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1)[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', '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, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 9, 6, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [12, 3, 12, 3, 3, 1, 1, 1, 1, 1, 1, 4, 4, 13, 13, 13, 13, 13, 1, 12, 16, 16, 16, 12, 12, 12, 3, 2, 2, 2, 1, 1, 13, 1, 1, 16, 16, 16, 16, 16, 16] 26 rigid atoms, others: [33, 34, 5, 6, 7, 8, 9, 10, 18, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 35, 36, 37, 38, 39, 40]) total number of confs: 86 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074101 /scratch/stefan/7916156/working /scratch/stefan/7916156 mkdir: created directory `1' /scratch/stefan/7916156/working/building/REAL250005074101/1 /scratch/stefan/7916156/working/building/REAL250005074101 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 1 (index: 213) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/213 `/scratch/stefan/7916156/working/3D/213' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1)N(C)C) `REAL250005074101.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005074101.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074101/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074101 none C[C@H](C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', '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, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 10, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 17, 33, 17, 17, 14, 14, 14, 14, 7, 1, 7, 1, 1, 1, 1, 1, 1, 14, 33, 35, 35, 33, 33, 33, 17, 14, 14, 14, 14, 14, 1, 14, 14, 35, 35, 35, 35, 35, 35] 35 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 108 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074101 none C[C@H](C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', '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, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 10, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [15, 3, 15, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 14, 14, 14, 14, 14, 1, 15, 19, 19, 15, 15, 15, 3, 2, 2, 2, 1, 1, 14, 1, 1, 19, 19, 19, 19, 19, 19] 35 rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 18, 29, 30] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 34, 35, 36, 37, 38, 39]) total number of confs: 93 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074101 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074101 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 1: /scratch/stefan/7916156/working/building/REAL250005074101/1.* 0: /scratch/stefan/7916156/working/building/REAL250005074101/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074101 Building REAL250005074102 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074102' /scratch/stefan/7916156/working/building/REAL250005074102 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074102 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074102/0 /scratch/stefan/7916156/working/building/REAL250005074102 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 214) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/214 `/scratch/stefan/7916156/working/3D/214' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC=CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074102.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074102/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074102 none CC=CC=CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [60, 60, 58, 58, 25, 25, 25, 18, 18, 18, 17, 7, 1, 7, 1, 1, 1, 1, 1, 1, 18, 60, 60, 60, 60, 60, 58, 58, 25, 18, 18, 18, 18, 17, 1, 18, 18] 60 rigid atoms, others: [34, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36]) total number of confs: 165 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074102 none CC=CC=CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 18, 18, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 17, 17, 17, 17, 17, 1, 29, 29, 29, 29, 29, 18, 18, 3, 2, 2, 2, 1, 1, 18, 1, 1] 60 rigid atoms, others: [32, 33, 35, 36, 7, 8, 9, 10, 11, 12, 20] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34]) total number of confs: 112 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074102 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074102 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074102/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074102 Building REAL250005074103 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074103' /scratch/stefan/7916156/working/building/REAL250005074103 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074103 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074103/0 /scratch/stefan/7916156/working/building/REAL250005074103 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 215) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/215 `/scratch/stefan/7916156/working/3D/215' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC=CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074103.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074103/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074103 none COCC=CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 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', '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, 1, 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, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 167 conformations in input total number of sets (complete confs): 167 using faster count positions algorithm for large data unique positions, atoms: [167, 163, 94, 94, 26, 26, 26, 20, 20, 20, 19, 9, 1, 9, 1, 1, 1, 1, 1, 1, 20, 167, 167, 167, 163, 163, 94, 94, 26, 20, 20, 20, 20, 19, 1, 20, 20] 167 rigid atoms, others: [34, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36]) total number of confs: 588 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074103 none COCC=CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 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', '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, 1, 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, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [96, 66, 19, 19, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 19, 19, 19, 19, 19, 1, 96, 96, 96, 66, 66, 19, 19, 3, 2, 2, 2, 1, 1, 20, 1, 1] 167 rigid atoms, others: [32, 33, 35, 36, 7, 8, 9, 10, 11, 12, 20] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34]) total number of confs: 315 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074103 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074103 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074103/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074103 Building REAL250005074104 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074104' /scratch/stefan/7916156/working/building/REAL250005074104 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074104 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074104/0 /scratch/stefan/7916156/working/building/REAL250005074104 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 216) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/216 `/scratch/stefan/7916156/working/3D/216' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2CCO2)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074104.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074104.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074104/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074104 none CC1(NC(=O)C2CCO2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [22, 13, 13, 1, 13, 1, 1, 1, 1, 22, 22, 22, 43, 43, 53, 53, 53, 53, 53, 22, 22, 22, 22, 13, 1, 1, 1, 1, 1, 22, 22, 53, 22, 22] 53 rigid atoms, others: [3, 5, 6, 7, 8, 24, 25, 26, 27, 28] set([0, 1, 2, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33]) total number of confs: 145 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074104 none CC1(NC(=O)C2CCO2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 3, 3, 3, 22, 22, 22, 1, 1, 1, 6, 6, 23, 23, 23, 23, 23, 1, 2, 2, 2, 3, 22, 22, 22, 22, 22, 1, 1, 23, 1, 1] 53 rigid atoms, others: [0, 1, 2, 33, 32, 9, 10, 11, 19, 29, 30] set([3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31]) total number of confs: 90 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.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: REAL250005074104 none CC1(NC(=O)C2CCO2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [23, 23, 23, 35, 35, 35, 53, 53, 53, 23, 9, 1, 9, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 35, 53, 53, 53, 53, 53, 23, 23, 1, 23, 23] 53 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33]) total number of confs: 141 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074104 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074104 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074104/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074104 Building REAL250005074105 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074105' /scratch/stefan/7916156/working/building/REAL250005074105 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074105 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074105/0 /scratch/stefan/7916156/working/building/REAL250005074105 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 217) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/217 `/scratch/stefan/7916156/working/3D/217' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)CCN=[N+]=[N-])CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074105.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074105/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074105 none CC1(NC(=O)CCN=[N+]=[N-])CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.2', 'N.1', 'N.1', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 8, 8, 8, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 17, 26, 26, 26, 109, 157, 201, 201, 16, 5, 1, 5, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 26, 109, 109, 157, 157, 17, 16, 1, 17, 17] 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, 32, 33]) total number of confs: 721 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074105 none CC1(NC(=O)CCN=[N+]=[N-])CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.2', 'N.1', 'N.1', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 8, 8, 8, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 3, 19, 46, 143, 143, 1, 1, 1, 6, 6, 16, 16, 16, 16, 16, 1, 2, 2, 2, 3, 19, 19, 46, 46, 1, 1, 17, 1, 1] 201 rigid atoms, others: [0, 1, 2, 33, 32, 10, 11, 12, 20, 29, 30] set([3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 31]) total number of confs: 362 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074105 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074105 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074105/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074105 Building REAL250005074106 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074106' /scratch/stefan/7916156/working/building/REAL250005074106 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074106 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074106/0 /scratch/stefan/7916156/working/building/REAL250005074106 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 218) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/218 `/scratch/stefan/7916156/working/3D/218' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCOCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074106.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074106/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074106 none C#CCOCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 164, 110, 26, 26, 26, 21, 21, 21, 21, 7, 1, 7, 1, 1, 1, 1, 1, 1, 21, 201, 201, 201, 110, 110, 26, 21, 21, 21, 21, 21, 1, 21, 21] 201 rigid atoms, others: [32, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34]) total number of confs: 666 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074106 none C#CCOCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [121, 121, 69, 22, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 21, 21, 21, 21, 21, 1, 121, 121, 121, 22, 22, 3, 2, 2, 2, 1, 1, 21, 1, 1] 201 rigid atoms, others: [33, 34, 7, 8, 9, 10, 11, 12, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32]) total number of confs: 432 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074106 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074106 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074106/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074106 Building REAL250005074107 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074107' /scratch/stefan/7916156/working/building/REAL250005074107 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074107 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074107/0 /scratch/stefan/7916156/working/building/REAL250005074107 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 219) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/219 `/scratch/stefan/7916156/working/3D/219' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC1C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074107.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074107/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074107 none CC1=CC1C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 92 conformations in input total number of sets (complete confs): 92 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 25, 2, 2, 2, 1, 1, 1, 1, 1, 1, 6, 6, 23, 23, 23, 23, 23, 1, 25, 25, 25, 25, 25, 2, 2, 2, 2, 1, 1, 23, 1, 1] 92 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 19, 29, 30] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31]) total number of confs: 96 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074107 none CC1=CC1C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 92 conformations in input total number of sets (complete confs): 92 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 13, 13, 13, 25, 25, 25, 25, 73, 73, 92, 92, 92, 92, 92, 25, 2, 2, 2, 1, 1, 13, 25, 25, 25, 25, 25, 92, 25, 25] 92 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 258 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074107 none CC1=CC1C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 31, 31, 31, 23, 23, 23, 23, 8, 1, 8, 1, 1, 1, 1, 1, 1, 23, 92, 92, 92, 92, 92, 31, 23, 23, 23, 23, 23, 1, 23, 23] 92 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33]) total number of confs: 235 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074107 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074107 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074107/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074107 Building REAL250005074108 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074108' /scratch/stefan/7916156/working/building/REAL250005074108 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074108 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074108/0 /scratch/stefan/7916156/working/building/REAL250005074108 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 220) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/220 `/scratch/stefan/7916156/working/3D/220' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074108.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074108/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074108 none CN(C)C(=O)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 8, 5, 1, 11, 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, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 20, 30, 20, 20, 17, 17, 17, 17, 8, 1, 8, 1, 1, 1, 1, 1, 1, 17, 30, 30, 30, 30, 30, 30, 20, 17, 17, 17, 17, 17, 1, 17, 17] 30 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: 81 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074108 none CN(C)C(=O)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 8, 5, 1, 11, 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, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [10, 9, 10, 3, 9, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 17, 17, 17, 17, 17, 1, 10, 10, 10, 10, 10, 10, 3, 2, 2, 2, 1, 1, 17, 1, 1] 30 rigid atoms, others: [32, 34, 35, 7, 8, 9, 10, 11, 12, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074108 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074108 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074108/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074108 Building REAL250005074109 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074109' /scratch/stefan/7916156/working/building/REAL250005074109 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074109 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074109/0 /scratch/stefan/7916156/working/building/REAL250005074109 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 221) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/221 `/scratch/stefan/7916156/working/3D/221' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSC=CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074109.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074109/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074109 none CSC=CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 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', 'C.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, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [49, 43, 43, 17, 17, 17, 14, 14, 14, 13, 6, 1, 6, 1, 1, 1, 1, 1, 1, 14, 49, 49, 49, 43, 43, 17, 14, 14, 14, 14, 13, 1, 14, 14] 49 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33]) total number of confs: 125 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074109 none CSC=CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 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', 'C.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, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [29, 14, 14, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 13, 13, 13, 13, 13, 1, 29, 29, 29, 14, 14, 3, 2, 2, 2, 1, 1, 14, 1, 1] 49 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 19, 29, 30] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074109 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074109 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074109/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074109 Building REAL250005074110 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074110' /scratch/stefan/7916156/working/building/REAL250005074110 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL250005074110 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074110/0 /scratch/stefan/7916156/working/building/REAL250005074110 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 222) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/222 `/scratch/stefan/7916156/working/3D/222' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@H+](C)CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074110.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074110/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074110 none CC[N@H+](C)CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 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', '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, 9, 6, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 13, 15, 15, 10, 10, 10, 10, 10, 10, 10, 4, 1, 4, 1, 1, 1, 1, 1, 1, 10, 16, 16, 16, 16, 16, 15, 15, 15, 13, 13, 10, 10, 10, 10, 10, 10, 1, 10, 10] 16 rigid atoms, others: [38, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40]) total number of confs: 54 number of broken/clashed sets: 14 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074110 none CC[N@H+](C)CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 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', '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, 9, 6, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [11, 10, 5, 10, 10, 2, 2, 2, 1, 1, 1, 1, 1, 1, 4, 4, 10, 10, 10, 10, 10, 1, 11, 11, 11, 11, 11, 10, 10, 10, 5, 5, 2, 2, 2, 2, 1, 1, 10, 1, 1] 16 rigid atoms, others: [36, 37, 39, 8, 9, 10, 11, 12, 13, 40, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38]) total number of confs: 71 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074110 /scratch/stefan/7916156/working /scratch/stefan/7916156 mkdir: created directory `1' /scratch/stefan/7916156/working/building/REAL250005074110/1 /scratch/stefan/7916156/working/building/REAL250005074110 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 1 (index: 223) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/223 `/scratch/stefan/7916156/working/3D/223' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@@H+](C)CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074110.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005074110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074110/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074110 none CC[N@@H+](C)CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 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', '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, 9, 6, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 19, 23, 23, 11, 11, 11, 10, 10, 10, 10, 5, 1, 5, 1, 1, 1, 1, 1, 1, 10, 23, 23, 23, 23, 23, 23, 23, 23, 19, 19, 11, 10, 10, 10, 10, 10, 1, 10, 10] 23 rigid atoms, others: [38, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40]) total number of confs: 80 number of broken/clashed sets: 21 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074110 none CC[N@@H+](C)CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 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', '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, 9, 6, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [18, 16, 7, 16, 15, 2, 2, 2, 1, 1, 1, 1, 1, 1, 4, 4, 10, 10, 10, 10, 10, 1, 18, 18, 18, 18, 18, 16, 16, 16, 7, 7, 2, 2, 2, 2, 1, 1, 10, 1, 1] 23 rigid atoms, others: [36, 37, 39, 8, 9, 10, 11, 12, 13, 40, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38]) total number of confs: 105 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074110 /scratch/stefan/7916156/working /scratch/stefan/7916156 mkdir: created directory `2' /scratch/stefan/7916156/working/building/REAL250005074110/2 /scratch/stefan/7916156/working/building/REAL250005074110 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 2 (index: 224) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/224 `/scratch/stefan/7916156/working/3D/224' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074110.mol2' -> `2.mol2' `temp.mol2' -> `REAL250005074110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074110/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074110 none CCN(C)CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 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', '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, 10, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [77, 76, 64, 76, 27, 27, 27, 24, 24, 24, 24, 10, 1, 10, 1, 1, 1, 1, 1, 1, 24, 77, 77, 77, 77, 77, 76, 76, 76, 64, 64, 27, 24, 24, 24, 24, 24, 1, 24, 24] 77 rigid atoms, others: [37, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39]) total number of confs: 265 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074110 none CCN(C)CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 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', '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, 10, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [33, 27, 15, 27, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 24, 24, 24, 24, 24, 1, 33, 33, 33, 33, 33, 27, 27, 27, 15, 15, 3, 2, 2, 2, 1, 1, 24, 1, 1] 77 rigid atoms, others: [35, 36, 38, 7, 8, 9, 10, 11, 12, 20, 39] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074110 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074110 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 1: /scratch/stefan/7916156/working/building/REAL250005074110/1.* 2: /scratch/stefan/7916156/working/building/REAL250005074110/2.* 0: /scratch/stefan/7916156/working/building/REAL250005074110/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074110 Building REAL250005074111 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074111' /scratch/stefan/7916156/working/building/REAL250005074111 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074111 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074111/0 /scratch/stefan/7916156/working/building/REAL250005074111 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 225) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/225 `/scratch/stefan/7916156/working/3D/225' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C1CC(C(=O)NC2(C)CN(C(=O)C3=CC(=O)[N-]O3)C2)C1) `REAL250005074111.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074111/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074111 none C=C1CC(C(=O)NC2(C)CN(C(=O)C3=CC(=O)[N-]O3)C2)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', '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, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 18, 18, 18, 18, 18, 1, 19, 19, 19, 19, 19, 19, 3, 2, 2, 2, 1, 1, 19, 1, 1, 19, 19] 55 rigid atoms, others: [33, 34, 6, 7, 8, 9, 10, 11, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 35, 36]) total number of confs: 80 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074111 none C=C1CC(C(=O)NC2(C)CN(C(=O)C3=CC(=O)[N-]O3)C2)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', '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, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 12, 12, 12, 19, 19, 19, 19, 51, 51, 55, 55, 55, 55, 55, 19, 1, 1, 1, 1, 1, 1, 12, 19, 19, 19, 19, 19, 55, 19, 19, 1, 1] 55 rigid atoms, others: [0, 1, 2, 3, 4, 35, 20, 21, 22, 23, 24, 25, 36] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 151 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.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: REAL250005074111 none C=C1CC(C(=O)NC2(C)CN(C(=O)C3=CC(=O)[N-]O3)C2)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', '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, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 55, 25, 25, 25, 19, 19, 19, 18, 8, 1, 8, 1, 1, 1, 1, 1, 1, 19, 55, 55, 55, 55, 55, 55, 25, 19, 19, 19, 19, 18, 1, 19, 19, 55, 55] 55 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: 152 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074111 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074111 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074111/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074111 Building REAL250005074112 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074112' /scratch/stefan/7916156/working/building/REAL250005074112 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074112 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074112/0 /scratch/stefan/7916156/working/building/REAL250005074112 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 226) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/226 `/scratch/stefan/7916156/working/3D/226' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2CCC2F)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074112.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074112/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074112 none CC1(NC(=O)C2CCC2F)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [25, 13, 13, 1, 13, 1, 1, 1, 1, 1, 25, 25, 25, 72, 72, 88, 88, 88, 88, 88, 25, 25, 25, 25, 13, 1, 1, 1, 1, 1, 1, 25, 25, 88, 25, 25] 88 rigid atoms, others: [3, 5, 6, 7, 8, 9, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31, 32, 33, 34, 35]) total number of confs: 240 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074112 none CC1(NC(=O)C2CCC2F)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 3, 25, 25, 25, 25, 1, 1, 1, 6, 6, 21, 21, 21, 21, 21, 1, 2, 2, 2, 3, 25, 25, 25, 25, 25, 25, 1, 1, 21, 1, 1] 88 rigid atoms, others: [0, 1, 2, 35, 32, 10, 11, 12, 34, 20, 31] set([3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33]) total number of confs: 94 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.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: REAL250005074112 none CC1(NC(=O)C2CCC2F)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 31, 31, 31, 88, 88, 88, 88, 21, 8, 1, 8, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 31, 88, 88, 88, 88, 88, 88, 21, 21, 1, 21, 21] 88 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: 238 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074112 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074112 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074112/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074112 Building REAL250005074113 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074113' /scratch/stefan/7916156/working/building/REAL250005074113 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074113 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074113/0 /scratch/stefan/7916156/working/building/REAL250005074113 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 227) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/227 `/scratch/stefan/7916156/working/3D/227' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CN=CN2)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074113.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074113/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074113 none CC1(NC(=O)C2=CN=CN2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [17, 11, 11, 1, 11, 1, 1, 1, 1, 1, 17, 17, 17, 38, 38, 45, 45, 45, 45, 45, 17, 17, 17, 17, 11, 1, 1, 1, 17, 17, 45, 17, 17] 45 rigid atoms, others: [3, 5, 6, 7, 8, 9, 25, 26, 27] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32]) total number of confs: 121 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074113 none CC1(NC(=O)C2=CN=CN2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 3, 3, 3, 17, 17, 17, 17, 1, 1, 1, 7, 7, 16, 16, 16, 16, 16, 1, 2, 2, 2, 3, 17, 17, 17, 1, 1, 16, 1, 1] 45 rigid atoms, others: [0, 1, 2, 32, 10, 11, 12, 20, 28, 29, 31] set([3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 30]) 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.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: REAL250005074113 none CC1(NC(=O)C2=CN=CN2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 24, 24, 24, 45, 45, 45, 45, 16, 7, 1, 7, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 24, 45, 45, 45, 16, 16, 1, 16, 16] 45 rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32]) total number of confs: 96 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074113 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074113 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074113/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074113 Building REAL250005074114 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074114' /scratch/stefan/7916156/working/building/REAL250005074114 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074114 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074114/0 /scratch/stefan/7916156/working/building/REAL250005074114 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 228) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/228 `/scratch/stefan/7916156/working/3D/228' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CCCO2)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074114.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074114/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074114 none CC1(NC(=O)C2=CCCO2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 5, 5, 12, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [13, 9, 9, 1, 9, 1, 1, 1, 1, 1, 13, 13, 13, 31, 31, 38, 38, 38, 38, 38, 13, 13, 13, 13, 9, 1, 1, 1, 1, 1, 13, 13, 38, 13, 13] 38 rigid atoms, others: [3, 5, 6, 7, 8, 9, 25, 26, 27, 28, 29] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31, 32, 33, 34]) total number of confs: 101 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074114 none CC1(NC(=O)C2=CCCO2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 5, 5, 12, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 3, 3, 3, 13, 13, 13, 13, 1, 1, 1, 6, 6, 16, 16, 16, 16, 16, 1, 2, 2, 2, 3, 13, 13, 13, 13, 13, 1, 1, 16, 1, 1] 38 rigid atoms, others: [0, 1, 2, 33, 10, 11, 12, 34, 20, 30, 31] set([3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074114 none CC1(NC(=O)C2=CCCO2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 5, 5, 12, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 25, 25, 25, 38, 38, 38, 38, 16, 9, 1, 9, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 25, 38, 38, 38, 38, 38, 16, 16, 1, 16, 16] 38 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: 88 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074114 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074114 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074114/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074114 Building REAL250005074115 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074115' /scratch/stefan/7916156/working/building/REAL250005074115 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074115 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074115/0 /scratch/stefan/7916156/working/building/REAL250005074115 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 229) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/229 `/scratch/stefan/7916156/working/3D/229' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@H](O)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074115.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074115/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074115 none CCC[C@H](O)C(=O)NC1(C)CN(C(=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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 366 conformations in input total number of sets (complete confs): 366 using faster count positions algorithm for large data unique positions, atoms: [122, 121, 96, 34, 96, 96, 34, 34, 25, 25, 25, 25, 11, 1, 11, 1, 1, 1, 1, 1, 1, 25, 122, 122, 122, 122, 122, 121, 121, 288, 34, 25, 25, 25, 25, 25, 1, 25, 25] 366 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: 766 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074115 none CCC[C@H](O)C(=O)NC1(C)CN(C(=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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 366 conformations in input total number of sets (complete confs): 366 using faster count positions algorithm for large data unique positions, atoms: [60, 54, 21, 2, 21, 21, 2, 2, 1, 1, 1, 1, 1, 1, 6, 6, 25, 25, 25, 25, 25, 1, 60, 60, 60, 60, 60, 55, 55, 63, 2, 2, 2, 2, 1, 1, 25, 1, 1] 366 rigid atoms, others: [34, 35, 37, 38, 8, 9, 10, 11, 12, 13, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36]) total number of confs: 361 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074115 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074115 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074115/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074115 Building REAL250005074116 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074116' /scratch/stefan/7916156/working/building/REAL250005074116 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074116 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074116/0 /scratch/stefan/7916156/working/building/REAL250005074116 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 230) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/230 `/scratch/stefan/7916156/working/3D/230' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](O)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074116.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074116.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074116/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074116 none CC(C)[C@H](O)C(=O)NC1(C)CN(C(=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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 165 conformations in input total number of sets (complete confs): 165 using faster count positions algorithm for large data unique positions, atoms: [55, 48, 55, 24, 48, 48, 24, 24, 18, 18, 18, 18, 9, 1, 9, 1, 1, 1, 1, 1, 1, 18, 55, 55, 55, 55, 55, 55, 55, 144, 24, 18, 18, 18, 18, 18, 1, 18, 18] 165 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: 342 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074116 none CC(C)[C@H](O)C(=O)NC1(C)CN(C(=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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 165 conformations in input total number of sets (complete confs): 165 using faster count positions algorithm for large data unique positions, atoms: [27, 15, 28, 3, 15, 15, 3, 3, 1, 1, 1, 1, 1, 1, 7, 7, 18, 18, 18, 18, 18, 1, 28, 28, 28, 28, 28, 28, 28, 45, 3, 2, 2, 2, 1, 1, 18, 1, 1] 165 rigid atoms, others: [34, 35, 37, 38, 8, 9, 10, 11, 12, 13, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36]) total number of confs: 199 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074116 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074116 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074116/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074116 Building REAL250005074117 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074117' /scratch/stefan/7916156/working/building/REAL250005074117 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074117 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074117/0 /scratch/stefan/7916156/working/building/REAL250005074117 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 231) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/231 `/scratch/stefan/7916156/working/3D/231' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC=CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074117.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074117/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074117 none CCOC=CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 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, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 91 conformations in input total number of sets (complete confs): 91 using faster count positions algorithm for large data unique positions, atoms: [91, 87, 63, 63, 19, 19, 19, 16, 16, 16, 15, 7, 1, 7, 1, 1, 1, 1, 1, 1, 16, 91, 91, 91, 91, 91, 63, 63, 19, 16, 16, 16, 16, 15, 1, 16, 16] 91 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: 220 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074117 none CCOC=CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 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, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [58, 49, 18, 18, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 15, 15, 15, 15, 15, 1, 58, 58, 58, 58, 58, 18, 18, 3, 2, 2, 2, 1, 1, 16, 1, 1] 91 rigid atoms, others: [32, 33, 35, 36, 7, 8, 9, 10, 11, 12, 20] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074117 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074117 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074117/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074117 Building REAL250005074118 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074118' /scratch/stefan/7916156/working/building/REAL250005074118 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074118 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074118/0 /scratch/stefan/7916156/working/building/REAL250005074118 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 232) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/232 `/scratch/stefan/7916156/working/3D/232' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074118.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074118/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074118 none C[C@@H](O)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [36, 25, 36, 36, 25, 25, 20, 20, 20, 20, 8, 1, 8, 1, 1, 1, 1, 1, 1, 20, 36, 36, 36, 108, 25, 20, 20, 20, 20, 20, 1, 20, 20] 108 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32]) total number of confs: 220 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074118 none C[C@@H](O)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [17, 3, 17, 17, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 20, 20, 20, 20, 20, 1, 17, 17, 17, 51, 3, 2, 2, 2, 1, 1, 20, 1, 1] 108 rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 19, 28, 29, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 30]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074118 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074118 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074118/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074118 Building REAL250005074119 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074119' /scratch/stefan/7916156/working/building/REAL250005074119 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074119 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074119/0 /scratch/stefan/7916156/working/building/REAL250005074119 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 233) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/233 `/scratch/stefan/7916156/working/3D/233' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)CCCCF)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074119.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074119.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074119/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074119 none CC1(NC(=O)CCCCF)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [17, 17, 17, 28, 28, 28, 74, 90, 137, 140, 16, 7, 1, 7, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 28, 74, 74, 105, 105, 134, 135, 139, 139, 17, 16, 1, 17, 17] 140 rigid atoms, others: [35, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37]) total number of confs: 686 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074119 none CC1(NC(=O)CCCCF)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 3, 3, 19, 28, 61, 91, 1, 1, 1, 5, 5, 16, 16, 16, 16, 16, 1, 2, 2, 2, 3, 19, 19, 36, 36, 59, 59, 91, 91, 1, 1, 17, 1, 1] 140 rigid atoms, others: [0, 1, 2, 36, 37, 33, 10, 11, 12, 34, 20] set([3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35]) total number of confs: 495 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074119 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074119 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074119/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074119 Building REAL250005074120 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074120' /scratch/stefan/7916156/working/building/REAL250005074120 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074120 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074120/0 /scratch/stefan/7916156/working/building/REAL250005074120 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 234) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/234 `/scratch/stefan/7916156/working/3D/234' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C=CCO)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074120.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074120/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074120 none CC1(NC(=O)C=CCO)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 5, 12, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 273 conformations in input total number of sets (complete confs): 273 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 24, 38, 38, 38, 76, 76, 91, 23, 9, 1, 9, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 38, 76, 76, 91, 91, 273, 24, 23, 1, 24, 24] 273 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33]) total number of confs: 583 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074120 none CC1(NC(=O)C=CCO)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 5, 12, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 273 conformations in input total number of sets (complete confs): 273 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 3, 3, 3, 15, 15, 54, 1, 1, 1, 6, 6, 23, 23, 23, 23, 23, 1, 2, 2, 2, 3, 15, 15, 54, 54, 162, 1, 1, 24, 1, 1] 273 rigid atoms, others: [0, 1, 2, 33, 32, 9, 10, 11, 19, 29, 30] set([3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31]) total number of confs: 385 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074120 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074120 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074120/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074120 Building REAL250005074121 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074121' /scratch/stefan/7916156/working/building/REAL250005074121 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074121 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074121/0 /scratch/stefan/7916156/working/building/REAL250005074121 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 235) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/235 `/scratch/stefan/7916156/working/3D/235' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)CCCCO)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074121.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074121.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074121/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074121 none CC1(NC(=O)CCCCO)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 18, 18, 30, 30, 30, 106, 140, 194, 201, 17, 5, 1, 5, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 30, 106, 106, 158, 158, 194, 195, 201, 201, 603, 18, 17, 1, 18, 18] 603 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: 1591 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074121 none CC1(NC(=O)CCCCO)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 3, 3, 3, 19, 32, 68, 130, 1, 1, 1, 6, 6, 17, 17, 17, 17, 17, 1, 2, 2, 2, 3, 19, 19, 40, 40, 70, 70, 134, 134, 390, 1, 1, 18, 1, 1] 603 rigid atoms, others: [0, 1, 2, 35, 37, 38, 10, 11, 12, 34, 20] set([3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36]) total number of confs: 1111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074121 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074121 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074121/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074121 Building REAL250005074122 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074122' /scratch/stefan/7916156/working/building/REAL250005074122 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074122 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074122/0 /scratch/stefan/7916156/working/building/REAL250005074122 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 236) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/236 `/scratch/stefan/7916156/working/3D/236' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(F)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074122.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074122.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074122/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074122 none COC(F)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 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', 'C.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, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [69, 68, 26, 68, 26, 26, 21, 21, 21, 20, 8, 1, 8, 1, 1, 1, 1, 1, 1, 21, 69, 69, 69, 68, 26, 21, 21, 21, 21, 20, 1, 21, 21] 69 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32]) total number of confs: 231 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074122 none COC(F)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 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', 'C.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, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [37, 19, 3, 19, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 20, 20, 20, 20, 20, 1, 37, 37, 37, 19, 3, 2, 2, 2, 1, 1, 21, 1, 1] 69 rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 19, 28, 29, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 30]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074122 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074122 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074122/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074122 Building REAL250005074123 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074123' /scratch/stefan/7916156/working/building/REAL250005074123 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074123 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074123/0 /scratch/stefan/7916156/working/building/REAL250005074123 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 237) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/237 `/scratch/stefan/7916156/working/3D/237' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C23CC2CC3)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074123.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074123.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074123/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074123 none CC1(NC(=O)C23CC2CC3)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 1, 11, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [13, 7, 7, 1, 7, 1, 1, 1, 1, 1, 13, 13, 13, 54, 54, 63, 63, 63, 63, 63, 13, 13, 13, 13, 7, 1, 1, 1, 1, 1, 1, 1, 13, 13, 63, 13, 13] 63 rigid atoms, others: [3, 5, 6, 7, 8, 9, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36]) total number of confs: 161 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074123 none CC1(NC(=O)C23CC2CC3)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 1, 11, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 3, 3, 3, 13, 13, 13, 13, 1, 1, 1, 7, 7, 14, 14, 14, 14, 14, 1, 2, 2, 2, 3, 13, 13, 13, 13, 13, 13, 13, 1, 1, 14, 1, 1] 63 rigid atoms, others: [0, 1, 2, 35, 36, 33, 32, 10, 11, 12, 20] set([3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34]) 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.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: REAL250005074123 none CC1(NC(=O)C23CC2CC3)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 1, 11, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [14, 14, 14, 18, 18, 18, 63, 63, 63, 63, 14, 7, 1, 7, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 18, 63, 63, 63, 63, 63, 63, 63, 14, 14, 1, 14, 14] 63 rigid atoms, others: [34, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36]) total number of confs: 100 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074123 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074123 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074123/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074123 Building REAL250005074124 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074124' /scratch/stefan/7916156/working/building/REAL250005074124 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074124 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074124/0 /scratch/stefan/7916156/working/building/REAL250005074124 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 238) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/238 `/scratch/stefan/7916156/working/3D/238' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C[C@H](C)CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074124.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074124/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074124 none C=C[C@H](C)CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 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', 'C.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, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 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, 104, 140, 139, 26, 26, 26, 19, 19, 19, 19, 8, 1, 8, 1, 1, 1, 1, 1, 1, 19, 140, 140, 140, 140, 140, 140, 104, 104, 26, 19, 19, 19, 19, 19, 1, 19, 19] 140 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: 564 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074124 none C=C[C@H](C)CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 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', 'C.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, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 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: [84, 63, 22, 63, 62, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 19, 19, 19, 19, 19, 1, 84, 84, 84, 63, 63, 63, 22, 22, 3, 2, 2, 2, 1, 1, 19, 1, 1] 140 rigid atoms, others: [34, 35, 37, 38, 8, 9, 10, 11, 12, 13, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36]) total number of confs: 361 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074124 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074124 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074124/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074124 Building REAL250005074125 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074125' /scratch/stefan/7916156/working/building/REAL250005074125 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074125 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074125/0 /scratch/stefan/7916156/working/building/REAL250005074125 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 239) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/239 `/scratch/stefan/7916156/working/3D/239' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C=CC2CC2)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074125.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074125/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074125 none CC1(NC(=O)C=CC2CC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [58, 46, 46, 10, 46, 10, 1, 1, 1, 1, 58, 58, 58, 114, 114, 120, 120, 120, 120, 120, 58, 58, 58, 58, 46, 10, 10, 1, 1, 1, 1, 1, 58, 58, 120, 58, 58] 120 rigid atoms, others: [6, 7, 8, 9, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 32, 33, 34, 35, 36]) total number of confs: 329 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074125 none CC1(NC(=O)C=CC2CC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 3, 3, 3, 20, 20, 58, 58, 1, 1, 1, 6, 6, 26, 26, 26, 26, 26, 1, 2, 2, 2, 3, 20, 20, 58, 58, 58, 58, 58, 1, 1, 26, 1, 1] 120 rigid atoms, others: [0, 1, 2, 35, 36, 33, 32, 10, 11, 12, 20] set([3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.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: REAL250005074125 none CC1(NC(=O)C=CC2CC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 26, 37, 37, 37, 98, 98, 120, 120, 26, 11, 1, 11, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 37, 98, 98, 120, 120, 120, 120, 120, 26, 26, 1, 26, 26] 120 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: 349 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074125 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074125 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074125/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074125 Building REAL250005074126 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074126' /scratch/stefan/7916156/working/building/REAL250005074126 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074126 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074126/0 /scratch/stefan/7916156/working/building/REAL250005074126 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 240) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/240 `/scratch/stefan/7916156/working/3D/240' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=C(CC)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074126.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074126.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074126/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074126 none CC=C(CC)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 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', 'C.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, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 117 conformations in input total number of sets (complete confs): 117 using faster count positions algorithm for large data unique positions, atoms: [102, 102, 37, 102, 117, 37, 37, 25, 25, 25, 25, 9, 1, 9, 1, 1, 1, 1, 1, 1, 25, 102, 102, 102, 102, 117, 117, 117, 117, 117, 37, 25, 25, 25, 25, 25, 1, 25, 25] 117 rigid atoms, others: [36, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 358 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074126 none CC=C(CC)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 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', 'C.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, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 117 conformations in input total number of sets (complete confs): 117 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 3, 24, 47, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 25, 25, 25, 25, 25, 1, 24, 24, 24, 24, 47, 47, 47, 47, 47, 3, 2, 2, 2, 1, 1, 25, 1, 1] 117 rigid atoms, others: [34, 35, 37, 38, 7, 8, 9, 10, 11, 12, 20] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36]) total number of confs: 228 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074126 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074126 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074126/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074126 Building REAL250005074127 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074127' /scratch/stefan/7916156/working/building/REAL250005074127 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074127 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074127/0 /scratch/stefan/7916156/working/building/REAL250005074127 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 241) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/241 `/scratch/stefan/7916156/working/3D/241' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CCC2)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074127.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074127/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074127 none CC1(NC(=O)C2=CCC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 8, 1, 8, 1, 1, 1, 1, 11, 11, 11, 18, 18, 20, 20, 20, 20, 20, 11, 11, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 20, 11, 11] 20 rigid atoms, others: [3, 5, 6, 7, 8, 24, 25, 26, 27, 28] set([0, 1, 2, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33]) total number of confs: 53 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074127 none CC1(NC(=O)C2=CCC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 11, 11, 11, 1, 1, 1, 6, 6, 13, 13, 13, 13, 13, 1, 2, 2, 2, 3, 11, 11, 11, 11, 11, 1, 1, 13, 1, 1] 20 rigid atoms, others: [0, 1, 2, 33, 32, 9, 10, 11, 19, 29, 30] set([3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074127 none CC1(NC(=O)C2=CCC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 20, 20, 20, 20, 20, 20, 13, 8, 1, 8, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 20, 20, 20, 20, 20, 20, 13, 13, 1, 13, 13] 20 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33]) total number of confs: 51 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074127 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074127 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074127/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074127 Building REAL250005074128 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074128' /scratch/stefan/7916156/working/building/REAL250005074128 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074128 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074128/0 /scratch/stefan/7916156/working/building/REAL250005074128 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 242) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/242 `/scratch/stefan/7916156/working/3D/242' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CON=CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074128.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074128.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074128/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074128 none CON=CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 18, 18, 18, 15, 15, 15, 14, 7, 1, 7, 1, 1, 1, 1, 1, 1, 15, 30, 30, 30, 30, 18, 15, 15, 15, 15, 14, 1, 15, 15] 30 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32]) total number of confs: 79 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074128 none CON=CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [17, 12, 12, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 14, 14, 14, 14, 14, 1, 17, 17, 17, 12, 3, 2, 2, 2, 1, 1, 15, 1, 1] 30 rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 19, 28, 29, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 30]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074128 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074128 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074128/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074128 Building REAL250005074129 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074129' /scratch/stefan/7916156/working/building/REAL250005074129 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074129 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074129/0 /scratch/stefan/7916156/working/building/REAL250005074129 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 243) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/243 `/scratch/stefan/7916156/working/3D/243' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)COCCO)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074129.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074129/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074129 none CC1(NC(=O)COCCO)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 1, 11, 5, 12, 5, 5, 12, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 3, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 30, 30, 30, 98, 161, 201, 201, 19, 6, 1, 6, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 30, 98, 98, 201, 201, 201, 201, 603, 19, 19, 1, 19, 19] 603 rigid atoms, others: [34, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36]) total number of confs: 1267 number of broken/clashed sets: 14 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074129 none CC1(NC(=O)COCCO)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 1, 11, 5, 12, 5, 5, 12, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 3, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 3, 3, 3, 24, 70, 125, 152, 1, 1, 1, 6, 6, 19, 19, 19, 19, 19, 1, 2, 2, 2, 3, 24, 24, 125, 125, 152, 152, 456, 1, 1, 19, 1, 1] 603 rigid atoms, others: [0, 1, 2, 35, 36, 33, 32, 10, 11, 12, 20] set([3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34]) total number of confs: 1057 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074129 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074129 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074129/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074129 Building REAL250005074130 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074130' /scratch/stefan/7916156/working/building/REAL250005074130 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074130 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074130/0 /scratch/stefan/7916156/working/building/REAL250005074130 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 244) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/244 `/scratch/stefan/7916156/working/3D/244' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=NOCC2)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074130.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074130/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074130 none CC1(NC(=O)C2=NOCC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 8, 12, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [18, 12, 12, 1, 12, 1, 1, 1, 1, 1, 18, 18, 18, 43, 43, 52, 52, 52, 52, 52, 18, 18, 18, 18, 12, 1, 1, 1, 1, 18, 18, 52, 18, 18] 52 rigid atoms, others: [3, 5, 6, 7, 8, 9, 25, 26, 27, 28] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33]) total number of confs: 142 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074130 none CC1(NC(=O)C2=NOCC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 8, 12, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 3, 3, 3, 18, 18, 18, 18, 1, 1, 1, 6, 6, 15, 15, 15, 15, 15, 1, 2, 2, 2, 3, 18, 18, 18, 18, 1, 1, 15, 1, 1] 52 rigid atoms, others: [0, 1, 2, 33, 32, 10, 11, 12, 20, 29, 30] set([3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 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.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: REAL250005074130 none CC1(NC(=O)C2=NOCC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 8, 12, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 15, 25, 25, 25, 52, 52, 52, 52, 15, 7, 1, 7, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 25, 52, 52, 52, 52, 15, 15, 1, 15, 15] 52 rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33]) total number of confs: 108 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074130 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074130 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074130/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074130 Building REAL250005074131 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074131' /scratch/stefan/7916156/working/building/REAL250005074131 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074131 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074131/0 /scratch/stefan/7916156/working/building/REAL250005074131 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 245) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/245 `/scratch/stefan/7916156/working/3D/245' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(O)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074131.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074131/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074131 none COCC(O)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 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', '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, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 198 conformations in input total number of sets (complete confs): 198 using faster count positions algorithm for large data unique positions, atoms: [66, 66, 55, 23, 55, 23, 23, 19, 19, 19, 19, 10, 1, 10, 1, 1, 1, 1, 1, 1, 19, 66, 66, 66, 66, 66, 55, 165, 23, 19, 19, 19, 19, 19, 1, 19, 19] 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, 35, 36]) total number of confs: 400 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074131 none COCC(O)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 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', '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, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 198 conformations in input total number of sets (complete confs): 198 using faster count positions algorithm for large data unique positions, atoms: [43, 34, 17, 3, 17, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 19, 19, 19, 19, 19, 1, 43, 43, 43, 34, 34, 17, 51, 3, 2, 2, 2, 1, 1, 19, 1, 1] 198 rigid atoms, others: [32, 33, 35, 36, 7, 8, 9, 10, 11, 12, 20] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34]) total number of confs: 244 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074131 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074131 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074131/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074131 Building REAL250005074132 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074132' /scratch/stefan/7916156/working/building/REAL250005074132 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074132 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074132/0 /scratch/stefan/7916156/working/building/REAL250005074132 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 246) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/246 `/scratch/stefan/7916156/working/3D/246' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)COC2CC2)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074132.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074132/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074132 none CC1(NC(=O)COC2CC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [131, 109, 109, 24, 109, 6, 1, 1, 1, 1, 131, 131, 131, 196, 196, 201, 201, 201, 201, 201, 131, 131, 131, 131, 109, 24, 24, 1, 1, 1, 1, 1, 131, 131, 201, 131, 131] 201 rigid atoms, others: [6, 7, 8, 9, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 32, 33, 34, 35, 36]) total number of confs: 594 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074132 none CC1(NC(=O)COC2CC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 3, 25, 82, 131, 131, 1, 1, 1, 6, 6, 18, 18, 18, 18, 18, 1, 2, 2, 2, 3, 25, 25, 131, 131, 131, 131, 131, 1, 1, 19, 1, 1] 201 rigid atoms, others: [0, 1, 2, 35, 36, 33, 32, 10, 11, 12, 20] set([3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34]) total number of confs: 369 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074132 none CC1(NC(=O)COC2CC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 19, 31, 31, 31, 128, 177, 201, 201, 18, 5, 1, 5, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 31, 128, 128, 201, 201, 201, 201, 201, 18, 19, 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: 645 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074132 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074132 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074132/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074132 Building REAL250005074133 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074133' /scratch/stefan/7916156/working/building/REAL250005074133 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074133 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074133/0 /scratch/stefan/7916156/working/building/REAL250005074133 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 247) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/247 `/scratch/stefan/7916156/working/3D/247' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=NC=CN2)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074133.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074133/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074133 none CC1(NC(=O)C2=NC=CN2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 8, 1, 1, 8, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 4, 1, 4, 1, 1, 1, 1, 1, 6, 6, 6, 16, 16, 23, 23, 23, 23, 23, 6, 6, 6, 6, 4, 1, 1, 1, 6, 6, 23, 6, 6] 23 rigid atoms, others: [3, 5, 6, 7, 8, 9, 25, 26, 27] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32]) total number of confs: 55 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074133 none CC1(NC(=O)C2=NC=CN2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 8, 1, 1, 8, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 3, 3, 3, 12, 12, 12, 12, 1, 1, 1, 6, 6, 18, 18, 18, 18, 18, 1, 2, 2, 2, 3, 12, 12, 12, 1, 1, 18, 1, 1] 31 rigid atoms, others: [0, 1, 2, 32, 10, 11, 12, 20, 28, 29, 31] set([3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 30]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074133 none CC1(NC(=O)C2=NC=CN2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 8, 1, 1, 8, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 23, 23, 23, 31, 31, 31, 31, 18, 8, 1, 8, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 23, 31, 31, 31, 18, 18, 1, 18, 18] 31 rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32]) total number of confs: 66 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074133 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074133 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074133/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074133 Building REAL250005074134 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074134' /scratch/stefan/7916156/working/building/REAL250005074134 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074134 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074134/0 /scratch/stefan/7916156/working/building/REAL250005074134 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 248) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/248 `/scratch/stefan/7916156/working/3D/248' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC=CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074134.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074134/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074134 none CCCC=CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 158 conformations in input total number of sets (complete confs): 158 using faster count positions algorithm for large data unique positions, atoms: [158, 147, 96, 96, 24, 24, 24, 17, 17, 17, 16, 8, 1, 8, 1, 1, 1, 1, 1, 1, 17, 158, 158, 158, 158, 158, 147, 147, 96, 96, 24, 17, 17, 17, 17, 16, 1, 17, 17] 158 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: 591 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074134 none CCCC=CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 158 conformations in input total number of sets (complete confs): 158 using faster count positions algorithm for large data unique positions, atoms: [76, 64, 20, 20, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 16, 16, 16, 16, 16, 1, 80, 80, 80, 80, 80, 64, 64, 20, 20, 3, 2, 2, 2, 1, 1, 17, 1, 1] 158 rigid atoms, others: [34, 35, 37, 38, 7, 8, 9, 10, 11, 12, 20] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36]) total number of confs: 382 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074134 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074134 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074134/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074134 Building REAL250005074135 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074135' /scratch/stefan/7916156/working/building/REAL250005074135 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074135 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074135/0 /scratch/stefan/7916156/working/building/REAL250005074135 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 249) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/249 `/scratch/stefan/7916156/working/3D/249' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=C(F)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074135.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074135.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074135/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074135 none CC=C(F)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 21, 33, 21, 21, 15, 15, 15, 14, 8, 1, 8, 1, 1, 1, 1, 1, 1, 15, 33, 33, 33, 33, 21, 15, 15, 15, 15, 14, 1, 15, 15] 33 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32]) total number of confs: 93 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074135 none CC=C(F)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [15, 15, 3, 15, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 14, 14, 14, 14, 14, 1, 15, 15, 15, 15, 3, 2, 2, 2, 1, 1, 15, 1, 1] 33 rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 19, 28, 29, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 30]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074135 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074135 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074135/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074135 Building REAL250005074136 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074136' /scratch/stefan/7916156/working/building/REAL250005074136 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074136 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074136/0 /scratch/stefan/7916156/working/building/REAL250005074136 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 250) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/250 `/scratch/stefan/7916156/working/3D/250' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CO)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074136.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074136/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074136 none CCC(CO)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 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', 'C.3', 'H', 'H', '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, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 282 conformations in input total number of sets (complete confs): 282 using faster count positions algorithm for large data unique positions, atoms: [89, 74, 25, 74, 94, 25, 25, 22, 22, 22, 22, 10, 1, 10, 1, 1, 1, 1, 1, 1, 22, 91, 91, 91, 91, 91, 74, 94, 94, 282, 25, 22, 22, 22, 21, 22, 1, 22, 22] 282 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: 754 number of broken/clashed sets: 43 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074136 none CCC(CO)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 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', 'C.3', 'H', 'H', '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, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 282 conformations in input total number of sets (complete confs): 282 using faster count positions algorithm for large data unique positions, atoms: [23, 17, 3, 17, 37, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 21, 21, 21, 21, 21, 1, 27, 27, 27, 27, 27, 17, 37, 37, 111, 3, 2, 2, 2, 1, 1, 22, 1, 1] 282 rigid atoms, others: [34, 35, 37, 38, 7, 8, 9, 10, 11, 12, 20] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36]) total number of confs: 374 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074136 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074136 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074136/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074136 Building REAL250005074137 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074137' /scratch/stefan/7916156/working/building/REAL250005074137 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074137 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074137/0 /scratch/stefan/7916156/working/building/REAL250005074137 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 251) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/251 `/scratch/stefan/7916156/working/3D/251' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CO)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074137.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074137/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074137 none CC(CO)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 174 conformations in input total number of sets (complete confs): 174 using faster count positions algorithm for large data unique positions, atoms: [55, 25, 55, 58, 25, 25, 22, 22, 22, 21, 8, 1, 8, 1, 1, 1, 1, 1, 1, 22, 55, 55, 55, 55, 58, 58, 174, 25, 22, 22, 22, 22, 21, 1, 22, 22] 174 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: 367 number of broken/clashed sets: 22 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074137 none CC(CO)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 174 conformations in input total number of sets (complete confs): 174 using faster count positions algorithm for large data unique positions, atoms: [15, 3, 15, 26, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 21, 21, 21, 21, 21, 1, 15, 15, 15, 15, 26, 26, 78, 3, 2, 2, 2, 1, 1, 22, 1, 1] 174 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33]) total number of confs: 224 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074137 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074137 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074137/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074137 Building REAL250005074138 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074138' /scratch/stefan/7916156/working/building/REAL250005074138 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074138 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074138/0 /scratch/stefan/7916156/working/building/REAL250005074138 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 252) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/252 `/scratch/stefan/7916156/working/3D/252' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CON=C2)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074138.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074138.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074138/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074138 none CC1(NC(=O)C2=CON=C2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 12, 8, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 9, 9, 9, 33, 33, 42, 42, 42, 42, 42, 9, 9, 9, 9, 5, 1, 1, 9, 9, 42, 9, 9] 42 rigid atoms, others: [3, 5, 6, 7, 8, 9, 25, 26] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31]) total number of confs: 109 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074138 none CC1(NC(=O)C2=CON=C2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 12, 8, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 1, 1, 1, 6, 6, 13, 13, 13, 13, 13, 1, 2, 2, 2, 3, 9, 9, 1, 1, 14, 1, 1] 42 rigid atoms, others: [0, 1, 2, 10, 11, 12, 20, 27, 28, 30, 31] set([3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 29]) 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.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: REAL250005074138 none CC1(NC(=O)C2=CON=C2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 12, 8, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [14, 14, 14, 23, 23, 23, 42, 42, 42, 42, 13, 5, 1, 5, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 23, 42, 42, 13, 14, 1, 14, 14] 42 rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31]) total number of confs: 100 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074138 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074138 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074138/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074138 Building REAL250005074139 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074139' /scratch/stefan/7916156/working/building/REAL250005074139 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074139 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074139/0 /scratch/stefan/7916156/working/building/REAL250005074139 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 253) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/253 `/scratch/stefan/7916156/working/3D/253' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)[C@@H]2C[C@H]2CF)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074139.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074139/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074139 none CC1(NC(=O)[C@@H]2C[C@H]2CF)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 15, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 152 conformations in input total number of sets (complete confs): 152 using faster count positions algorithm for large data unique positions, atoms: [25, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 10, 25, 25, 25, 88, 88, 143, 143, 143, 143, 143, 25, 25, 25, 25, 13, 1, 1, 10, 10, 25, 25, 143, 25, 25] 152 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 27, 28] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 363 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074139 none CC1(NC(=O)[C@@H]2C[C@H]2CF)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 15, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 152 conformations in input total number of sets (complete confs): 152 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 3, 3, 3, 25, 25, 25, 25, 25, 86, 1, 1, 1, 6, 6, 24, 24, 24, 24, 24, 1, 2, 2, 2, 3, 25, 25, 86, 86, 1, 1, 24, 1, 1] 152 rigid atoms, others: [0, 1, 2, 34, 32, 12, 13, 14, 35, 22, 31] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 33]) total number of confs: 342 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.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: REAL250005074139 none CC1(NC(=O)[C@@H]2C[C@H]2CF)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 15, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 152 conformations in input total number of sets (complete confs): 152 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 24, 39, 39, 39, 143, 143, 143, 143, 143, 152, 24, 9, 1, 9, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 39, 143, 143, 152, 152, 24, 24, 1, 24, 24] 152 rigid atoms, others: [33, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35]) total number of confs: 427 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074139 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074139 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074139/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074139 Building REAL250005074140 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074140' /scratch/stefan/7916156/working/building/REAL250005074140 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074140 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074140/0 /scratch/stefan/7916156/working/building/REAL250005074140 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 254) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/254 `/scratch/stefan/7916156/working/3D/254' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=COCC2)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074140.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074140/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074140 none CC1(NC(=O)C2=COCC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 12, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [16, 9, 9, 1, 9, 1, 1, 1, 1, 1, 16, 16, 16, 47, 47, 54, 54, 54, 54, 54, 16, 16, 16, 16, 9, 1, 1, 1, 1, 1, 16, 16, 54, 16, 16] 54 rigid atoms, others: [3, 5, 6, 7, 8, 9, 25, 26, 27, 28, 29] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31, 32, 33, 34]) total number of confs: 149 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074140 none CC1(NC(=O)C2=COCC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 12, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 3, 3, 3, 16, 16, 16, 16, 1, 1, 1, 6, 6, 14, 14, 14, 14, 14, 1, 2, 2, 2, 3, 16, 16, 16, 16, 16, 1, 1, 14, 1, 1] 54 rigid atoms, others: [0, 1, 2, 33, 10, 11, 12, 34, 20, 30, 31] set([3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32]) 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.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: REAL250005074140 none CC1(NC(=O)C2=COCC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 12, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [14, 14, 14, 22, 22, 22, 54, 54, 54, 54, 14, 6, 1, 6, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 22, 54, 54, 54, 54, 54, 14, 14, 1, 14, 14] 54 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: 107 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074140 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074140 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074140/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074140 Building REAL250005074141 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074141' /scratch/stefan/7916156/working/building/REAL250005074141 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074141 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074141/0 /scratch/stefan/7916156/working/building/REAL250005074141 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 255) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/255 `/scratch/stefan/7916156/working/3D/255' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074141.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074141/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074141 none C[C@H](O)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [36, 25, 36, 36, 25, 25, 20, 20, 20, 19, 7, 1, 7, 1, 1, 1, 1, 1, 1, 20, 36, 36, 36, 108, 25, 20, 20, 20, 20, 19, 1, 20, 20] 108 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32]) total number of confs: 222 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074141 none C[C@H](O)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [17, 3, 17, 17, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 19, 19, 19, 19, 19, 1, 17, 17, 17, 51, 3, 2, 2, 2, 1, 1, 20, 1, 1] 108 rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 19, 28, 29, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 30]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074141 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074141 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074141/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074141 Building REAL250005074142 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074142' /scratch/stefan/7916156/working/building/REAL250005074142 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074142 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074142/0 /scratch/stefan/7916156/working/building/REAL250005074142 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 256) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/256 `/scratch/stefan/7916156/working/3D/256' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2C=CCC2)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074142.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074142/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074142 none CC1(NC(=O)C2C=CCC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 1, 1, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 98 conformations in input total number of sets (complete confs): 98 using faster count positions algorithm for large data unique positions, atoms: [25, 13, 13, 1, 13, 1, 1, 1, 1, 1, 25, 25, 25, 78, 78, 98, 98, 98, 98, 98, 25, 25, 25, 25, 13, 1, 1, 1, 1, 1, 1, 1, 25, 25, 98, 25, 25] 98 rigid atoms, others: [3, 5, 6, 7, 8, 9, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36]) total number of confs: 260 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074142 none CC1(NC(=O)C2C=CCC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 1, 1, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 98 conformations in input total number of sets (complete confs): 98 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 3, 3, 3, 25, 25, 25, 25, 1, 1, 1, 6, 6, 22, 22, 22, 22, 22, 1, 2, 2, 2, 3, 25, 25, 25, 25, 25, 25, 25, 1, 1, 22, 1, 1] 98 rigid atoms, others: [0, 1, 2, 35, 36, 33, 32, 10, 11, 12, 20] set([3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34]) total number of confs: 95 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.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: REAL250005074142 none CC1(NC(=O)C2C=CCC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 1, 1, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 98 conformations in input total number of sets (complete confs): 98 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 35, 35, 35, 98, 98, 98, 98, 22, 8, 1, 8, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 35, 98, 98, 98, 98, 98, 98, 98, 22, 22, 1, 22, 22] 98 rigid atoms, others: [34, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36]) total number of confs: 261 number of broken/clashed sets: 5 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074142 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074142 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074142/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074142 Building REAL250005074143 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074143' /scratch/stefan/7916156/working/building/REAL250005074143 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074143 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074143/0 /scratch/stefan/7916156/working/building/REAL250005074143 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 257) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/257 `/scratch/stefan/7916156/working/3D/257' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)C(C)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074143.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074143/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074143 none CC(O)C(C)C(=O)NC1(C)CN(C(=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, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [59, 52, 60, 20, 52, 20, 20, 18, 18, 18, 18, 9, 1, 9, 1, 1, 1, 1, 1, 1, 18, 60, 60, 60, 60, 180, 52, 52, 52, 52, 20, 18, 18, 18, 18, 18, 1, 18, 18] 180 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: 410 number of broken/clashed sets: 15 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074143 none CC(O)C(C)C(=O)NC1(C)CN(C(=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, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [24, 15, 26, 3, 15, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 18, 18, 18, 18, 18, 1, 26, 26, 26, 26, 78, 15, 15, 15, 15, 3, 2, 2, 2, 1, 1, 18, 1, 1] 180 rigid atoms, others: [34, 35, 37, 38, 7, 8, 9, 10, 11, 12, 20] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36]) total number of confs: 230 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074143 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074143 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074143/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074143 Building REAL250005074144 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074144' /scratch/stefan/7916156/working/building/REAL250005074144 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074144 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074144/0 /scratch/stefan/7916156/working/building/REAL250005074144 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 258) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/258 `/scratch/stefan/7916156/working/3D/258' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C1CC1C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074144.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074144/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074144 none C=C1CC1C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 23, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 20, 20, 20, 20, 20, 1, 23, 23, 23, 23, 23, 3, 2, 2, 2, 1, 1, 21, 1, 1] 74 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 19, 29, 30] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31]) total number of confs: 91 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074144 none C=C1CC1C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 13, 13, 13, 23, 23, 23, 23, 60, 60, 74, 74, 74, 74, 74, 23, 1, 1, 1, 1, 1, 13, 23, 23, 23, 23, 23, 74, 23, 23] 74 rigid atoms, others: [0, 1, 2, 3, 4, 20, 21, 22, 23, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.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: REAL250005074144 none C=C1CC1C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [74, 74, 74, 28, 28, 28, 21, 21, 21, 20, 7, 1, 7, 1, 1, 1, 1, 1, 1, 21, 74, 74, 74, 74, 74, 28, 21, 21, 21, 21, 20, 1, 21, 21] 74 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33]) total number of confs: 191 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074144 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074144 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074144/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074144 Building REAL250005074145 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074145' /scratch/stefan/7916156/working/building/REAL250005074145 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074145 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074145/0 /scratch/stefan/7916156/working/building/REAL250005074145 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 259) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/259 `/scratch/stefan/7916156/working/3D/259' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CF)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074145.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074145/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074145 none CC(CF)C(=O)NC1(C)CN(C(=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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [69, 22, 69, 71, 22, 22, 18, 18, 18, 17, 6, 1, 6, 1, 1, 1, 1, 1, 1, 18, 69, 69, 69, 69, 71, 71, 22, 18, 18, 18, 18, 17, 1, 18, 18] 71 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: 256 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074145 none CC(CF)C(=O)NC1(C)CN(C(=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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [20, 3, 20, 36, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 17, 17, 17, 17, 17, 1, 20, 20, 20, 20, 36, 36, 3, 2, 2, 2, 1, 1, 18, 1, 1] 71 rigid atoms, others: [33, 34, 6, 7, 8, 9, 10, 11, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074145 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074145 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074145/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074145 Building REAL250005074146 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074146' /scratch/stefan/7916156/working/building/REAL250005074146 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074146 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074146/0 /scratch/stefan/7916156/working/building/REAL250005074146 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 260) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/260 `/scratch/stefan/7916156/working/3D/260' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074146.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074146/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074146 none C=C(C)CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [72, 72, 72, 24, 24, 24, 21, 21, 21, 21, 10, 1, 10, 1, 1, 1, 1, 1, 1, 21, 72, 72, 72, 72, 72, 72, 72, 24, 21, 21, 21, 21, 21, 1, 21, 21] 72 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: 234 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074146 none C=C(C)CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [27, 21, 27, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 21, 21, 21, 21, 21, 1, 27, 27, 27, 27, 27, 21, 21, 3, 2, 2, 2, 1, 1, 21, 1, 1] 72 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074146 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074146 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074146/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074146 Building REAL250005074147 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074147' /scratch/stefan/7916156/working/building/REAL250005074147 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074147 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074147/0 /scratch/stefan/7916156/working/building/REAL250005074147 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 261) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/261 `/scratch/stefan/7916156/working/3D/261' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCSCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074147.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074147/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074147 none CCSCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 178, 130, 32, 32, 32, 26, 26, 26, 26, 10, 1, 10, 1, 1, 1, 1, 1, 1, 26, 201, 201, 201, 201, 201, 130, 130, 32, 26, 26, 26, 26, 26, 1, 26, 26] 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: 660 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074147 none CCSCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [117, 82, 23, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 26, 26, 26, 26, 26, 1, 117, 117, 117, 117, 117, 23, 23, 3, 2, 2, 2, 1, 1, 26, 1, 1] 201 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33]) total number of confs: 391 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074147 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074147 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074147/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074147 Building REAL250005074148 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074148' /scratch/stefan/7916156/working/building/REAL250005074148 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074148 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074148/0 /scratch/stefan/7916156/working/building/REAL250005074148 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 262) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/262 `/scratch/stefan/7916156/working/3D/262' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)=C(C)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074148.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074148.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074148/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074148 none CC(C)=C(C)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 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', 'C.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, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 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, 35, 21, 35, 21, 21, 16, 16, 16, 16, 8, 1, 8, 1, 1, 1, 1, 1, 1, 16, 35, 35, 35, 35, 35, 35, 35, 35, 35, 21, 16, 16, 16, 15, 16, 1, 16, 16] 35 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: 99 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074148 none CC(C)=C(C)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 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', 'C.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, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 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: [12, 12, 12, 3, 12, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 15, 15, 15, 15, 15, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 3, 2, 2, 2, 1, 1, 16, 1, 1] 35 rigid atoms, others: [34, 35, 37, 38, 7, 8, 9, 10, 11, 12, 20] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074148 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074148 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074148/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074148 Building REAL250005074149 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074149' /scratch/stefan/7916156/working/building/REAL250005074149 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074149 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074149/0 /scratch/stefan/7916156/working/building/REAL250005074149 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 263) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/263 `/scratch/stefan/7916156/working/3D/263' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(O)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074149.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074149/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074149 none CCCC(O)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 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', 'C.3', 'H', 'H', '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, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 294 conformations in input total number of sets (complete confs): 294 using faster count positions algorithm for large data unique positions, atoms: [98, 97, 68, 24, 68, 24, 24, 22, 22, 22, 22, 9, 1, 9, 1, 1, 1, 1, 1, 1, 22, 98, 98, 98, 98, 98, 97, 97, 68, 204, 24, 22, 22, 22, 22, 22, 1, 22, 22] 294 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: 594 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074149 none CCCC(O)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 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', 'C.3', 'H', 'H', '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, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 294 conformations in input total number of sets (complete confs): 294 using faster count positions algorithm for large data unique positions, atoms: [46, 38, 19, 3, 19, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 22, 22, 22, 22, 22, 1, 46, 46, 46, 46, 45, 39, 39, 19, 57, 3, 2, 2, 2, 1, 1, 22, 1, 1] 294 rigid atoms, others: [34, 35, 37, 38, 7, 8, 9, 10, 11, 12, 20] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36]) total number of confs: 296 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074149 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074149 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074149/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074149 Building REAL250005074150 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074150' /scratch/stefan/7916156/working/building/REAL250005074150 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074150 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074150/0 /scratch/stefan/7916156/working/building/REAL250005074150 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 264) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/264 `/scratch/stefan/7916156/working/3D/264' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(O)CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074150.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074150/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074150 none CCC(O)CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 139, 114, 139, 25, 25, 25, 19, 19, 19, 19, 7, 1, 7, 1, 1, 1, 1, 1, 1, 19, 142, 142, 142, 142, 142, 139, 417, 114, 114, 25, 19, 19, 19, 19, 19, 1, 19, 19] 426 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: 965 number of broken/clashed sets: 23 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074150 none CCC(O)CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [66, 49, 20, 50, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 19, 19, 19, 19, 19, 1, 66, 66, 66, 66, 65, 50, 150, 20, 20, 3, 2, 2, 2, 1, 1, 19, 1, 1] 426 rigid atoms, others: [34, 35, 37, 38, 7, 8, 9, 10, 11, 12, 20] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36]) total number of confs: 475 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074150 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074150 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074150/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074150 Building REAL250005074151 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074151' /scratch/stefan/7916156/working/building/REAL250005074151 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074151 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074151/0 /scratch/stefan/7916156/working/building/REAL250005074151 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 265) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/265 `/scratch/stefan/7916156/working/3D/265' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(Cl)=CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074151.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074151.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074151/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074151 none CC(Cl)=CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 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', 'C.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, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 24, 24, 24, 19, 19, 19, 18, 8, 1, 8, 1, 1, 1, 1, 1, 1, 19, 48, 48, 48, 48, 24, 19, 19, 19, 19, 18, 1, 19, 19] 48 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32]) total number of confs: 126 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074151 none CC(Cl)=CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 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', 'C.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, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 18, 18, 18, 18, 18, 1, 16, 16, 16, 16, 3, 2, 2, 2, 1, 1, 19, 1, 1] 48 rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 19, 28, 29, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 30]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074151 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074151 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074151/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074151 Building REAL250005074152 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074152' /scratch/stefan/7916156/working/building/REAL250005074152 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074152 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074152/0 /scratch/stefan/7916156/working/building/REAL250005074152 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 266) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/266 `/scratch/stefan/7916156/working/3D/266' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074152.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074152/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074152 none CC=CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 23, 23, 23, 18, 18, 18, 17, 6, 1, 6, 1, 1, 1, 1, 1, 1, 18, 31, 31, 31, 31, 31, 23, 18, 18, 18, 18, 17, 1, 18, 18] 31 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: 84 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074152 none CC=CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 17, 17, 17, 17, 17, 1, 13, 13, 13, 13, 13, 3, 2, 2, 2, 1, 1, 18, 1, 1] 31 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 18, 28, 29, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074152 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074152 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074152/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074152 Building REAL250005074153 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074153' /scratch/stefan/7916156/working/building/REAL250005074153 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074153 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074153/0 /scratch/stefan/7916156/working/building/REAL250005074153 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 267) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/267 `/scratch/stefan/7916156/working/3D/267' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)[C@H]2C[C@@H](O)C2)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074153.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074153/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074153 none CC1(NC(=O)[C@H]2C[C@@H](O)C2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 249 conformations in input total number of sets (complete confs): 249 using faster count positions algorithm for large data unique positions, atoms: [22, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 70, 70, 83, 83, 83, 83, 83, 22, 22, 22, 22, 13, 1, 1, 3, 1, 1, 22, 22, 83, 22, 22] 249 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 11, 27, 28, 30, 31] set([0, 1, 2, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 32, 33, 34, 35, 36]) total number of confs: 218 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074153 none CC1(NC(=O)[C@H]2C[C@@H](O)C2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 249 conformations in input total number of sets (complete confs): 249 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 3, 3, 3, 22, 22, 22, 22, 22, 22, 1, 1, 1, 6, 6, 25, 25, 25, 25, 25, 1, 2, 2, 2, 3, 22, 22, 66, 22, 22, 1, 1, 25, 1, 1] 249 rigid atoms, others: [0, 1, 2, 35, 36, 33, 32, 12, 13, 14, 22] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34]) total number of confs: 158 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.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: REAL250005074153 none CC1(NC(=O)[C@H]2C[C@@H](O)C2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 249 conformations in input total number of sets (complete confs): 249 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 25, 35, 35, 35, 83, 83, 83, 83, 83, 83, 25, 10, 1, 10, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 35, 83, 83, 249, 83, 83, 25, 25, 1, 25, 25] 249 rigid atoms, others: [34, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36]) total number of confs: 475 number of broken/clashed sets: 6 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074153 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074153 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074153/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074153 Building REAL250005074154 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074154' /scratch/stefan/7916156/working/building/REAL250005074154 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074154 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074154/0 /scratch/stefan/7916156/working/building/REAL250005074154 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 268) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/268 `/scratch/stefan/7916156/working/3D/268' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H]1C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074154.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074154/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074154 none C[C@@H]1C[C@H]1C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 21, 3, 21, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 17, 17, 17, 17, 17, 1, 21, 21, 21, 21, 21, 3, 2, 2, 2, 1, 1, 17, 1, 1] 56 rigid atoms, others: [32, 34, 35, 8, 9, 10, 11, 12, 13, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33]) total number of confs: 81 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074154 none C[C@@H]1C[C@H]1C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 21, 21, 21, 21, 48, 48, 56, 56, 56, 56, 56, 21, 2, 2, 2, 1, 1, 12, 21, 21, 21, 21, 21, 56, 21, 21] 56 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 25, 26] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.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: REAL250005074154 none C[C@@H]1C[C@H]1C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 56, 56, 23, 56, 23, 23, 18, 18, 18, 17, 7, 1, 7, 1, 1, 1, 1, 1, 1, 18, 56, 56, 56, 56, 56, 23, 18, 18, 18, 17, 17, 1, 18, 18] 56 rigid atoms, others: [33, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35]) total number of confs: 156 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074154 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074154 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074154/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074154 Building REAL250005074155 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074155' /scratch/stefan/7916156/working/building/REAL250005074155 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074155 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074155/0 /scratch/stefan/7916156/working/building/REAL250005074155 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 269) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/269 `/scratch/stefan/7916156/working/3D/269' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074155.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074155/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074155 none CNC(=O)CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 122, 147, 32, 32, 32, 26, 26, 26, 26, 10, 1, 10, 1, 1, 1, 1, 1, 1, 26, 147, 147, 147, 147, 122, 122, 32, 26, 26, 26, 26, 26, 1, 26, 26] 147 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: 497 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074155 none CNC(=O)CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [86, 86, 25, 86, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 26, 26, 26, 26, 26, 1, 86, 86, 86, 86, 25, 25, 3, 2, 2, 2, 1, 1, 26, 1, 1] 147 rigid atoms, others: [32, 34, 35, 7, 8, 9, 10, 11, 12, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33]) total number of confs: 285 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074155 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074155 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074155/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074155 Building REAL250005074156 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074156' /scratch/stefan/7916156/working/building/REAL250005074156 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074156 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074156/0 /scratch/stefan/7916156/working/building/REAL250005074156 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 270) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/270 `/scratch/stefan/7916156/working/3D/270' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC=CCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074156.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074156/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074156 none C=CC=CCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 136, 31, 31, 31, 23, 23, 23, 23, 10, 1, 10, 1, 1, 1, 1, 1, 1, 23, 179, 179, 179, 179, 179, 136, 136, 31, 23, 23, 23, 23, 23, 1, 23, 23] 179 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: 625 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074156 none C=CC=CCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 179 conformations in input total number of sets (complete confs): 179 using faster count positions algorithm for large data unique positions, atoms: [111, 105, 105, 25, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 23, 23, 23, 23, 23, 1, 111, 111, 111, 105, 105, 25, 25, 3, 2, 2, 2, 1, 1, 23, 1, 1] 179 rigid atoms, others: [32, 33, 35, 36, 7, 8, 9, 10, 11, 12, 20] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34]) total number of confs: 345 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074156 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074156 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074156/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074156 Building REAL250005074157 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074157' /scratch/stefan/7916156/working/building/REAL250005074157 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074157 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074157/0 /scratch/stefan/7916156/working/building/REAL250005074157 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 271) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/271 `/scratch/stefan/7916156/working/3D/271' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)CCC(N)=O)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074157.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074157/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074157 none CC1(NC(=O)CCC(N)=O)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 1, 8, 11, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 4, 6, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 15, 17, 17, 17, 10, 3, 1, 3, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 15, 15, 17, 17, 17, 17, 11, 10, 1, 11, 11] 17 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: 57 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074157 none CC1(NC(=O)CCC(N)=O)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 1, 8, 11, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 4, 6, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 3, 3, 3, 9, 13, 15, 15, 1, 1, 1, 4, 4, 10, 10, 10, 10, 10, 1, 2, 2, 2, 3, 9, 9, 13, 13, 15, 15, 1, 1, 11, 1, 1] 17 rigid atoms, others: [0, 1, 2, 35, 32, 10, 11, 12, 34, 20, 31] set([3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074157 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074157 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074157/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074157 Building REAL250005074158 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074158' /scratch/stefan/7916156/working/building/REAL250005074158 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074158 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074158/0 /scratch/stefan/7916156/working/building/REAL250005074158 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 272) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/272 `/scratch/stefan/7916156/working/3D/272' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)CCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074158.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074158/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074158 none CC(O)CCC(=O)NC1(C)CN(C(=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, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 255 conformations in input total number of sets (complete confs): 255 using faster count positions algorithm for large data unique positions, atoms: [85, 73, 85, 62, 26, 26, 26, 23, 23, 23, 22, 9, 1, 9, 1, 1, 1, 1, 1, 1, 23, 85, 85, 85, 83, 255, 79, 79, 62, 62, 26, 23, 23, 23, 23, 22, 1, 23, 23] 255 rigid atoms, others: [36, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 612 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074158 none CC(O)CCC(=O)NC1(C)CN(C(=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, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 255 conformations in input total number of sets (complete confs): 255 using faster count positions algorithm for large data unique positions, atoms: [51, 27, 51, 18, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 22, 22, 22, 22, 22, 1, 51, 51, 51, 48, 153, 33, 33, 18, 18, 3, 2, 2, 2, 1, 1, 23, 1, 1] 255 rigid atoms, others: [34, 35, 37, 38, 7, 8, 9, 10, 11, 12, 20] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36]) total number of confs: 448 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074158 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074158 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074158/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074158 Building REAL250005074159 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074159' /scratch/stefan/7916156/working/building/REAL250005074159 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074159 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074159/0 /scratch/stefan/7916156/working/building/REAL250005074159 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 273) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/273 `/scratch/stefan/7916156/working/3D/273' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCC(C)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074159.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074159/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074159 none C#CCC(C)C(=O)NC1(C)CN(C(=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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [116, 116, 86, 27, 86, 27, 27, 23, 23, 23, 22, 9, 1, 9, 1, 1, 1, 1, 1, 1, 23, 116, 116, 116, 86, 86, 86, 86, 27, 23, 23, 23, 23, 22, 1, 23, 23] 116 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: 459 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074159 none C#CCC(C)C(=O)NC1(C)CN(C(=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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 21, 3, 21, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 22, 22, 22, 22, 22, 1, 48, 48, 48, 21, 21, 21, 21, 3, 2, 2, 2, 1, 1, 23, 1, 1] 116 rigid atoms, others: [32, 33, 35, 36, 7, 8, 9, 10, 11, 12, 20] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34]) total number of confs: 230 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074159 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074159 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074159/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074159 Building REAL250005074160 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074160' /scratch/stefan/7916156/working/building/REAL250005074160 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074160 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074160/0 /scratch/stefan/7916156/working/building/REAL250005074160 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 274) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/274 `/scratch/stefan/7916156/working/3D/274' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCO)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074160.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074160/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074160 none CC(CCO)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 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', 'C.3', 'H', 'H', '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, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 240 conformations in input total number of sets (complete confs): 240 using faster count positions algorithm for large data unique positions, atoms: [69, 26, 69, 79, 80, 26, 26, 22, 22, 22, 21, 7, 1, 7, 1, 1, 1, 1, 1, 1, 22, 69, 69, 69, 69, 80, 80, 79, 80, 240, 26, 22, 22, 22, 22, 21, 1, 22, 22] 240 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: 538 number of broken/clashed sets: 21 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074160 none CC(CCO)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 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', 'C.3', 'H', 'H', '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, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 240 conformations in input total number of sets (complete confs): 240 using faster count positions algorithm for large data unique positions, atoms: [19, 3, 19, 36, 46, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 21, 21, 21, 21, 21, 1, 19, 19, 19, 19, 37, 37, 45, 46, 138, 3, 2, 2, 2, 1, 1, 22, 1, 1] 240 rigid atoms, others: [34, 35, 37, 38, 7, 8, 9, 10, 11, 12, 20] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36]) total number of confs: 378 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074160 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074160 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074160/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074160 Building REAL250005074161 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074161' /scratch/stefan/7916156/working/building/REAL250005074161 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074161 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074161/0 /scratch/stefan/7916156/working/building/REAL250005074161 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 275) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/275 `/scratch/stefan/7916156/working/3D/275' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)[C@H](O)CF)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074161.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074161/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074161 none CC1(NC(=O)[C@H](O)CF)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', '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, 8, 1, 11, 5, 7, 12, 5, 15, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 342 conformations in input total number of sets (complete confs): 342 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 23, 35, 35, 35, 93, 93, 93, 114, 23, 8, 1, 8, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 35, 279, 114, 114, 23, 23, 1, 23, 23] 342 rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32]) total number of confs: 727 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074161 none CC1(NC(=O)[C@H](O)CF)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', '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, 8, 1, 11, 5, 7, 12, 5, 15, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 342 conformations in input total number of sets (complete confs): 342 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 3, 3, 3, 23, 23, 23, 46, 1, 1, 1, 6, 6, 23, 23, 23, 23, 23, 1, 2, 2, 2, 3, 69, 46, 46, 1, 1, 23, 1, 1] 342 rigid atoms, others: [0, 1, 2, 32, 10, 11, 12, 20, 28, 29, 31] set([3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 30]) total number of confs: 294 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074161 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074161 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074161/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074161 Building REAL250005074162 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074162' /scratch/stefan/7916156/working/building/REAL250005074162 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074162 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074162/0 /scratch/stefan/7916156/working/building/REAL250005074162 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 276) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/276 `/scratch/stefan/7916156/working/3D/276' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)CC2CC2)C1) `REAL250005074162.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074162/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074162 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)CC2CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [13, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 13, 13, 13, 26, 26, 52, 75, 75, 13, 13, 13, 13, 7, 1, 13, 13, 52, 52, 75, 75, 75, 75, 75, 13, 13] 75 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 24] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 304 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074162 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)CC2CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 3, 3, 3, 13, 13, 13, 13, 13, 1, 1, 1, 6, 6, 23, 38, 38, 1, 2, 2, 2, 3, 13, 1, 1, 23, 23, 38, 38, 38, 38, 38, 1, 1] 75 rigid atoms, others: [0, 1, 2, 34, 35, 11, 12, 13, 19, 25, 26] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074162 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)CC2CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 38, 62, 62, 62, 75, 75, 75, 75, 75, 38, 19, 3, 19, 1, 1, 1, 1, 38, 38, 38, 38, 62, 75, 38, 38, 3, 3, 1, 1, 1, 1, 1, 38, 38] 75 rigid atoms, others: [32, 33, 15, 16, 17, 18, 29, 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, 34, 35]) total number of confs: 197 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074162 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074162 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074162/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074162 Building REAL250005074163 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074163' /scratch/stefan/7916156/working/building/REAL250005074163 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074163 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074163/0 /scratch/stefan/7916156/working/building/REAL250005074163 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 277) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/277 `/scratch/stefan/7916156/working/3D/277' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(F)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074163.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074163/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074163 none CC(C)(F)C(=O)N1CC(C)(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 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 8, 13, 13, 6, 8, 6, 6, 4, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 6, 13, 13, 13, 13, 13, 13, 6, 6, 6, 6, 6, 4, 1, 6, 6] 13 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: 50 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074163 none CC(C)(F)C(=O)N1CC(C)(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 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 7, 1, 2, 1, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 6, 1, 7, 7, 7, 7, 7, 7, 1, 1, 2, 2, 2, 3, 6, 1, 1] 13 rigid atoms, others: [33, 34, 4, 6, 7, 8, 9, 10, 19, 26, 27] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32]) total number of confs: 42 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074163 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074163 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074163/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074163 Building REAL250005074164 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074164' /scratch/stefan/7916156/working/building/REAL250005074164 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074164 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074164/0 /scratch/stefan/7916156/working/building/REAL250005074164 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 278) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/278 `/scratch/stefan/7916156/working/3D/278' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(F)(F)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074164.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074164/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074164 none CC(F)(F)C(=O)N1CC(C)(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 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [25, 13, 25, 25, 6, 13, 6, 6, 4, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 6, 25, 25, 25, 6, 6, 6, 6, 6, 4, 1, 6, 6] 25 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: 98 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074164 none CC(F)(F)C(=O)N1CC(C)(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 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [18, 6, 18, 18, 1, 6, 1, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 6, 1, 18, 18, 18, 1, 1, 2, 2, 2, 3, 6, 1, 1] 25 rigid atoms, others: [4, 6, 7, 8, 9, 10, 19, 23, 24, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 25, 26, 27, 28, 29]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074164 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074164 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074164/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074164 Building REAL250005074165 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074165' /scratch/stefan/7916156/working/building/REAL250005074165 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074165 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074165/0 /scratch/stefan/7916156/working/building/REAL250005074165 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 279) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/279 `/scratch/stefan/7916156/working/3D/279' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074165.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074165/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074165 none COCC(=O)N1CC(C)(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 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [28, 27, 13, 8, 13, 8, 8, 6, 8, 6, 1, 6, 1, 1, 1, 1, 1, 1, 8, 28, 28, 28, 27, 27, 8, 8, 8, 8, 8, 6, 1, 8, 8] 28 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: 96 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074165 none COCC(=O)N1CC(C)(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 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [22, 15, 4, 1, 4, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 1, 22, 22, 22, 15, 15, 1, 1, 2, 2, 2, 3, 8, 1, 1] 28 rigid atoms, others: [32, 3, 5, 6, 7, 8, 9, 18, 24, 25, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074165 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074165 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074165/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074165 Building REAL250005074166 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074166' /scratch/stefan/7916156/working/building/REAL250005074166 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074166 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074166/0 /scratch/stefan/7916156/working/building/REAL250005074166 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 280) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/280 `/scratch/stefan/7916156/working/3D/280' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074166.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074166/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074166 none CCCC(=O)N1CC(C)(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 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [45, 42, 20, 12, 20, 12, 12, 8, 12, 8, 1, 8, 1, 1, 1, 1, 1, 1, 12, 45, 45, 45, 45, 45, 42, 42, 12, 12, 12, 12, 12, 8, 1, 12, 12] 45 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: 163 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074166 none CCCC(=O)N1CC(C)(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 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [27, 18, 6, 1, 6, 1, 1, 1, 1, 1, 3, 3, 3, 12, 12, 12, 12, 12, 1, 28, 28, 28, 27, 27, 18, 18, 1, 1, 2, 2, 2, 3, 12, 1, 1] 45 rigid atoms, others: [33, 34, 3, 5, 6, 7, 8, 9, 18, 26, 27] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074166 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074166 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074166/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074166 Building REAL250005074167 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074167' /scratch/stefan/7916156/working/building/REAL250005074167 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074167 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074167/0 /scratch/stefan/7916156/working/building/REAL250005074167 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 281) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/281 `/scratch/stefan/7916156/working/3D/281' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=CC=CO2)C1) `REAL250005074167.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074167/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074167 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=CC=CO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [9, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 9, 9, 9, 22, 22, 34, 34, 34, 34, 9, 9, 9, 9, 7, 1, 9, 9, 34, 34, 34, 9, 9] 34 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 25] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 79 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074167 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=CC=CO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 1, 1, 1, 6, 6, 16, 16, 16, 16, 1, 2, 2, 2, 3, 9, 1, 1, 16, 16, 16, 1, 1] 34 rigid atoms, others: [0, 1, 2, 32, 11, 12, 13, 20, 26, 27, 31] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074167 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=CC=CO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [17, 16, 17, 31, 31, 31, 34, 34, 34, 34, 34, 16, 9, 1, 9, 1, 1, 1, 1, 1, 16, 17, 17, 17, 31, 34, 16, 16, 1, 1, 1, 16, 16] 34 rigid atoms, others: [13, 15, 16, 17, 18, 19, 28, 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, 31, 32]) total number of confs: 97 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074167 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074167 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074167/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074167 Building REAL250005074168 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074168' /scratch/stefan/7916156/working/building/REAL250005074168 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074168 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074168/0 /scratch/stefan/7916156/working/building/REAL250005074168 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 282) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/282 `/scratch/stefan/7916156/working/3D/282' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074168.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074168.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074168/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074168 none CC(=O)NCC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [80, 80, 80, 72, 21, 9, 21, 9, 9, 7, 9, 7, 1, 7, 1, 1, 1, 1, 1, 1, 9, 80, 80, 80, 80, 72, 72, 9, 9, 9, 9, 9, 7, 1, 9, 9] 80 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: 299 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074168 none CC(=O)NCC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [66, 66, 66, 33, 6, 1, 6, 1, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 1, 66, 66, 66, 66, 33, 33, 1, 1, 2, 2, 2, 3, 9, 1, 1] 80 rigid atoms, others: [34, 35, 5, 7, 8, 9, 10, 11, 20, 27, 28] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074168 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074168 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074168/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074168 Building REAL250005074169 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074169' /scratch/stefan/7916156/working/building/REAL250005074169 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074169 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074169/0 /scratch/stefan/7916156/working/building/REAL250005074169 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 283) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/283 `/scratch/stefan/7916156/working/3D/283' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074169.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074169/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074169 none CC(C)CC(=O)N1CC(C)(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 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [29, 28, 29, 17, 9, 17, 9, 9, 7, 9, 7, 1, 7, 1, 1, 1, 1, 1, 1, 9, 29, 29, 29, 29, 29, 29, 29, 28, 28, 9, 9, 9, 9, 9, 7, 1, 9, 9] 29 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: 107 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074169 none CC(C)CC(=O)N1CC(C)(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 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [19, 17, 20, 5, 1, 5, 1, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 1, 20, 20, 20, 20, 20, 20, 20, 17, 17, 1, 1, 2, 2, 2, 3, 9, 1, 1] 29 rigid atoms, others: [4, 37, 6, 7, 8, 9, 10, 19, 36, 29, 30] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074169 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074169 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074169/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074169 Building REAL250005074170 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074170' /scratch/stefan/7916156/working/building/REAL250005074170 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074170 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074170/0 /scratch/stefan/7916156/working/building/REAL250005074170 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 284) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/284 `/scratch/stefan/7916156/working/3D/284' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC1C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074170.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074170/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074170 none CC1CC1C(=O)N1CC(C)(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 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 4, 1, 4, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 1, 12, 12, 12, 12, 12, 12, 12, 1, 1, 2, 2, 2, 2, 7, 1, 1] 20 rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 10, 19, 27, 28] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 47 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074170 none CC1CC1C(=O)N1CC(C)(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 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, 6, 6, 12, 12, 12, 12, 17, 17, 17, 20, 20, 20, 20, 20, 12, 2, 2, 2, 1, 1, 1, 1, 12, 12, 12, 12, 12, 17, 20, 12, 12] 20 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 25, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074170 none CC1CC1C(=O)N1CC(C)(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 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 11, 7, 11, 7, 7, 6, 7, 6, 1, 6, 1, 1, 1, 1, 1, 1, 7, 20, 20, 20, 20, 20, 20, 20, 7, 7, 8, 8, 8, 6, 1, 7, 7] 20 rigid atoms, others: [33, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35]) total number of confs: 65 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074170 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074170 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074170/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074170 Building REAL250005074171 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074171' /scratch/stefan/7916156/working/building/REAL250005074171 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074171 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074171/0 /scratch/stefan/7916156/working/building/REAL250005074171 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 285) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/285 `/scratch/stefan/7916156/working/3D/285' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074171.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074171/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074171 none CCOCC(=O)N1CC(C)(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 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [84, 82, 64, 23, 10, 23, 10, 10, 8, 10, 8, 1, 8, 1, 1, 1, 1, 1, 1, 10, 84, 84, 84, 84, 84, 64, 64, 10, 10, 10, 10, 10, 8, 1, 10, 10] 84 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: 275 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074171 none CCOCC(=O)N1CC(C)(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 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [66, 61, 34, 6, 1, 6, 1, 1, 1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 10, 1, 67, 67, 67, 66, 66, 34, 34, 1, 1, 2, 2, 2, 3, 10, 1, 1] 84 rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 10, 19, 27, 28] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074171 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074171 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074171/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074171 Building REAL250005074172 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074172' /scratch/stefan/7916156/working/building/REAL250005074172 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074172 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074172/0 /scratch/stefan/7916156/working/building/REAL250005074172 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 286) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/286 `/scratch/stefan/7916156/working/3D/286' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)=CC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074172.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074172.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074172/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074172 none CC(C)=CC(=O)N1CC(C)(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 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 16, 8, 16, 8, 8, 6, 8, 6, 1, 6, 1, 1, 1, 1, 1, 1, 8, 25, 25, 25, 25, 25, 25, 25, 8, 8, 8, 8, 8, 6, 1, 8, 8] 25 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: 79 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074172 none CC(C)=CC(=O)N1CC(C)(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 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 6, 1, 6, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 1, 18, 18, 18, 18, 18, 18, 18, 1, 1, 2, 2, 2, 3, 8, 1, 1] 25 rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 10, 19, 27, 28] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074172 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074172 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074172/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074172 Building REAL250005074173 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074173' /scratch/stefan/7916156/working/building/REAL250005074173 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074173 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074173/0 /scratch/stefan/7916156/working/building/REAL250005074173 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 287) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/287 `/scratch/stefan/7916156/working/3D/287' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2CCCO2)C1) `REAL250005074173.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074173/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074173 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2CCCO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [11, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 11, 11, 11, 23, 23, 42, 42, 42, 42, 11, 11, 11, 11, 8, 1, 11, 11, 42, 42, 42, 42, 42, 42, 42, 11, 11] 42 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 25] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 119 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074173 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2CCCO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 3, 3, 3, 11, 11, 11, 11, 11, 1, 1, 1, 6, 6, 29, 29, 29, 29, 1, 2, 2, 2, 3, 11, 1, 1, 29, 29, 29, 29, 29, 29, 29, 1, 1] 42 rigid atoms, others: [0, 1, 2, 35, 36, 11, 12, 13, 20, 26, 27] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34]) 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.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: REAL250005074173 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2CCCO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [29, 29, 29, 39, 39, 39, 42, 42, 42, 42, 42, 29, 9, 1, 9, 1, 1, 1, 1, 1, 29, 29, 29, 29, 39, 42, 29, 29, 1, 1, 1, 1, 1, 1, 1, 29, 29] 42 rigid atoms, others: [32, 33, 34, 13, 15, 16, 17, 18, 19, 28, 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, 35, 36]) total number of confs: 92 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074173 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074173 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074173/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074173 Building REAL250005074174 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074174' /scratch/stefan/7916156/working/building/REAL250005074174 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074174 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074174/0 /scratch/stefan/7916156/working/building/REAL250005074174 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 288) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/288 `/scratch/stefan/7916156/working/3D/288' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSCC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074174.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074174/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074174 none CSCC(=O)N1CC(C)(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 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [36, 28, 18, 8, 18, 8, 8, 6, 8, 6, 1, 6, 1, 1, 1, 1, 1, 1, 8, 36, 36, 36, 28, 28, 8, 8, 8, 8, 8, 6, 1, 8, 8] 36 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32]) total number of confs: 107 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074174 none CSCC(=O)N1CC(C)(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 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [31, 19, 5, 1, 5, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 1, 31, 31, 31, 19, 19, 1, 1, 2, 2, 2, 3, 8, 1, 1] 36 rigid atoms, others: [32, 3, 5, 6, 7, 8, 9, 18, 24, 25, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074174 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074174 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074174/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074174 Building REAL250005074175 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074175' /scratch/stefan/7916156/working/building/REAL250005074175 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074175 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074175/0 /scratch/stefan/7916156/working/building/REAL250005074175 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 289) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/289 `/scratch/stefan/7916156/working/3D/289' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSCCC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074175.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074175/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074175 none CSCCC(=O)N1CC(C)(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 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [107, 70, 66, 23, 9, 23, 9, 9, 7, 9, 7, 1, 7, 1, 1, 1, 1, 1, 1, 9, 107, 107, 107, 70, 70, 66, 66, 9, 9, 9, 9, 9, 7, 1, 9, 9] 107 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: 322 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074175 none CSCCC(=O)N1CC(C)(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 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [84, 47, 37, 6, 1, 6, 1, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 1, 84, 84, 84, 47, 47, 37, 37, 1, 1, 2, 2, 2, 3, 9, 1, 1] 107 rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 10, 19, 27, 28] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 263 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074175 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074175 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074175/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074175 Building REAL250005074176 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074176' /scratch/stefan/7916156/working/building/REAL250005074176 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074176 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074176/0 /scratch/stefan/7916156/working/building/REAL250005074176 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 290) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/290 `/scratch/stefan/7916156/working/3D/290' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CCC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074176.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074176/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074176 none CC(C)CCC(=O)N1CC(C)(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 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [72, 67, 72, 61, 22, 9, 22, 9, 9, 8, 9, 8, 1, 8, 1, 1, 1, 1, 1, 1, 9, 72, 72, 72, 72, 72, 72, 72, 67, 67, 61, 61, 9, 9, 9, 9, 9, 8, 1, 9, 9] 72 rigid atoms, others: [38, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40]) total number of confs: 291 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074176 none CC(C)CCC(=O)N1CC(C)(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 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [50, 42, 53, 32, 6, 1, 6, 1, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 1, 53, 53, 50, 53, 53, 53, 53, 42, 42, 32, 32, 1, 1, 2, 2, 2, 3, 9, 1, 1] 72 rigid atoms, others: [32, 33, 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, 34, 35, 36, 37, 38]) total number of confs: 263 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074176 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074176 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074176/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074176 Building REAL250005074177 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074177' /scratch/stefan/7916156/working/building/REAL250005074177 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074177 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074177/0 /scratch/stefan/7916156/working/building/REAL250005074177 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 291) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/291 `/scratch/stefan/7916156/working/3D/291' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=CC=CN2)C1) `REAL250005074177.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074177/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074177 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=CC=CN2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [13, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 13, 13, 13, 32, 32, 54, 54, 54, 54, 13, 13, 13, 13, 7, 1, 13, 13, 54, 54, 54, 54, 13, 13] 54 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 25] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 130 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074177 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=CC=CN2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 3, 3, 3, 13, 13, 13, 13, 13, 1, 1, 1, 6, 6, 32, 32, 32, 32, 1, 2, 2, 2, 3, 13, 1, 1, 32, 32, 32, 32, 1, 1] 54 rigid atoms, others: [0, 1, 2, 33, 32, 11, 12, 13, 20, 26, 27] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30, 31]) total number of confs: 69 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.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: REAL250005074177 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=CC=CN2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 32, 49, 49, 49, 54, 54, 54, 54, 54, 32, 10, 1, 10, 1, 1, 1, 1, 1, 32, 32, 32, 32, 49, 54, 32, 32, 1, 1, 1, 1, 32, 32] 54 rigid atoms, others: [13, 15, 16, 17, 18, 19, 28, 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, 32, 33]) total number of confs: 131 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074177 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074177 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074177/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074177 Building REAL250005074178 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074178' /scratch/stefan/7916156/working/building/REAL250005074178 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074178 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074178/0 /scratch/stefan/7916156/working/building/REAL250005074178 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 292) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/292 `/scratch/stefan/7916156/working/3D/292' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=COC=C2)C1) `REAL250005074178.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074178/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074178 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=COC=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 1, 12, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [13, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 13, 13, 13, 25, 25, 62, 62, 62, 62, 13, 13, 13, 13, 6, 1, 13, 13, 62, 62, 62, 13, 13] 62 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 25] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 130 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074178 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=COC=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 1, 12, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 3, 3, 3, 13, 13, 13, 13, 13, 1, 1, 1, 6, 6, 36, 36, 36, 36, 1, 2, 2, 2, 3, 13, 1, 1, 36, 36, 36, 1, 1] 62 rigid atoms, others: [0, 1, 2, 32, 11, 12, 13, 20, 26, 27, 31] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30]) total number of confs: 73 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.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: REAL250005074178 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=COC=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 1, 12, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 36, 55, 55, 55, 62, 62, 62, 62, 62, 36, 9, 1, 9, 1, 1, 1, 1, 1, 36, 36, 36, 36, 55, 62, 36, 36, 1, 1, 1, 36, 36] 62 rigid atoms, others: [13, 15, 16, 17, 18, 19, 28, 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, 31, 32]) total number of confs: 144 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074178 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074178 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074178/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074178 Building REAL250005074179 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074179' /scratch/stefan/7916156/working/building/REAL250005074179 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074179 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074179/0 /scratch/stefan/7916156/working/building/REAL250005074179 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 293) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/293 `/scratch/stefan/7916156/working/3D/293' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074179.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074179/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074179 none CCCCCC(=O)N1CC(C)(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 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [137, 129, 98, 73, 19, 9, 19, 9, 9, 8, 9, 8, 1, 8, 1, 1, 1, 1, 1, 1, 9, 139, 140, 140, 140, 140, 131, 129, 104, 104, 73, 73, 9, 9, 9, 9, 9, 8, 1, 9, 9] 140 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: 667 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074179 none CCCCCC(=O)N1CC(C)(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 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [103, 83, 51, 35, 6, 1, 6, 1, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 1, 110, 115, 115, 114, 114, 84, 84, 57, 57, 35, 35, 1, 1, 2, 2, 2, 3, 9, 1, 1] 140 rigid atoms, others: [32, 33, 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, 34, 35, 36, 37, 38]) total number of confs: 634 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074179 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074179 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074179/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074179 Building REAL250005074180 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074180' /scratch/stefan/7916156/working/building/REAL250005074180 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074180 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074180/0 /scratch/stefan/7916156/working/building/REAL250005074180 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 294) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/294 `/scratch/stefan/7916156/working/3D/294' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)CC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074180.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074180/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074180 none CC(C)(C)CC(=O)N1CC(C)(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 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [29, 28, 29, 29, 18, 8, 18, 8, 8, 6, 8, 6, 1, 6, 1, 1, 1, 1, 1, 1, 8, 29, 29, 29, 29, 29, 29, 29, 29, 29, 28, 28, 8, 8, 8, 8, 8, 6, 1, 8, 8] 29 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: 101 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074180 none CC(C)(C)CC(=O)N1CC(C)(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 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [20, 17, 20, 20, 6, 1, 6, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 1, 21, 21, 21, 20, 20, 20, 21, 21, 21, 17, 17, 1, 1, 2, 2, 2, 3, 8, 1, 1] 29 rigid atoms, others: [32, 33, 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, 34, 35, 36, 37, 38]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074180 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074180 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074180/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074180 Building REAL250005074181 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074181' /scratch/stefan/7916156/working/building/REAL250005074181 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074181 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074181/0 /scratch/stefan/7916156/working/building/REAL250005074181 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 295) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/295 `/scratch/stefan/7916156/working/3D/295' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074181.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074181.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074181/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074181 none CCCCC(=O)N1CC(C)(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 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [99, 86, 77, 26, 10, 26, 10, 10, 7, 10, 7, 1, 7, 1, 1, 1, 1, 1, 1, 10, 99, 99, 99, 99, 99, 86, 86, 77, 77, 10, 10, 10, 10, 10, 7, 1, 10, 10] 99 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: 412 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074181 none CCCCC(=O)N1CC(C)(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 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [73, 46, 33, 6, 1, 6, 1, 1, 1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 10, 1, 73, 73, 73, 72, 72, 49, 49, 33, 33, 1, 1, 2, 2, 2, 3, 10, 1, 1] 99 rigid atoms, others: [4, 37, 6, 7, 8, 9, 10, 19, 36, 29, 30] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35]) total number of confs: 358 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074181 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074181 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074181/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074181 Building REAL250005074182 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074182' /scratch/stefan/7916156/working/building/REAL250005074182 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074182 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074182/0 /scratch/stefan/7916156/working/building/REAL250005074182 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 296) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/296 `/scratch/stefan/7916156/working/3D/296' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074182.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074182.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074182/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074182 none CC(C)C(=O)N1CC(C)(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 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 13, 17, 9, 13, 9, 9, 7, 9, 7, 1, 7, 1, 1, 1, 1, 1, 1, 9, 17, 17, 17, 17, 17, 17, 17, 9, 9, 9, 9, 9, 7, 1, 9, 9] 17 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: 59 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074182 none CC(C)C(=O)N1CC(C)(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 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 7, 1, 3, 1, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 1, 8, 8, 8, 7, 7, 7, 7, 1, 1, 2, 2, 2, 3, 9, 1, 1] 17 rigid atoms, others: [33, 34, 3, 5, 6, 7, 8, 9, 18, 26, 27] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32]) total number of confs: 50 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074182 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074182 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074182/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074182 Building REAL250005074183 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074183' /scratch/stefan/7916156/working/building/REAL250005074183 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074183 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074183/0 /scratch/stefan/7916156/working/building/REAL250005074183 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 297) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/297 `/scratch/stefan/7916156/working/3D/297' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074183.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074183/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074183 none CCC(C)C(=O)N1CC(C)(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 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 13, 25, 8, 13, 8, 8, 6, 8, 6, 1, 6, 1, 1, 1, 1, 1, 1, 8, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8, 8, 8, 8, 8, 6, 1, 8, 8] 25 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: 89 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074183 none CCC(C)C(=O)N1CC(C)(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 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [17, 15, 6, 15, 1, 6, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 1, 18, 18, 18, 18, 18, 15, 15, 15, 15, 1, 1, 2, 2, 2, 3, 8, 1, 1] 25 rigid atoms, others: [4, 37, 6, 7, 8, 9, 10, 19, 36, 29, 30] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35]) total number of confs: 91 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074183 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074183 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074183/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074183 Building REAL250005074184 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074184' /scratch/stefan/7916156/working/building/REAL250005074184 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074184 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074184/0 /scratch/stefan/7916156/working/building/REAL250005074184 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 298) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/298 `/scratch/stefan/7916156/working/3D/298' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074184.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074184/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074184 none CCC(CC)C(=O)N1CC(C)(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 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [24, 23, 15, 23, 24, 7, 15, 7, 7, 5, 7, 5, 1, 5, 1, 1, 1, 1, 1, 1, 7, 24, 24, 24, 24, 24, 23, 25, 25, 25, 25, 25, 7, 7, 7, 7, 7, 5, 1, 7, 7] 26 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: 108 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074184 none CCC(CC)C(=O)N1CC(C)(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 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [15, 14, 6, 14, 18, 1, 6, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 1, 16, 16, 16, 16, 16, 14, 19, 19, 19, 19, 19, 1, 1, 2, 2, 2, 3, 7, 1, 1] 26 rigid atoms, others: [32, 33, 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, 34, 35, 36, 37, 38]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074184 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074184 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074184/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074184 Building REAL250005074185 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074185' /scratch/stefan/7916156/working/building/REAL250005074185 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005074185 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074185/0 /scratch/stefan/7916156/working/building/REAL250005074185 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 299) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/299 `/scratch/stefan/7916156/working/3D/299' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=NNC=C2)C1) `REAL250005074185.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074185/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074185 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=NNC=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 8, 8, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 10, 10, 10, 24, 24, 36, 36, 36, 36, 10, 10, 10, 10, 7, 1, 10, 10, 36, 36, 36, 10, 10] 36 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 25] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 89 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074185 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=NNC=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 8, 8, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 10, 1, 1, 1, 6, 6, 18, 18, 18, 18, 1, 2, 2, 2, 3, 10, 1, 1, 18, 18, 18, 1, 1] 36 rigid atoms, others: [0, 1, 2, 32, 11, 12, 13, 20, 26, 27, 31] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074185 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=NNC=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 8, 8, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 32, 32, 32, 36, 36, 36, 36, 36, 18, 10, 1, 10, 1, 1, 1, 1, 1, 18, 18, 18, 18, 32, 36, 18, 18, 1, 1, 1, 18, 18] 36 rigid atoms, others: [13, 15, 16, 17, 18, 19, 28, 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, 31, 32]) total number of confs: 98 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074185 /scratch/stefan/7916156/working /scratch/stefan/7916156 mkdir: created directory `1' /scratch/stefan/7916156/working/building/REAL250005074185/1 /scratch/stefan/7916156/working/building/REAL250005074185 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 1 (index: 300) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/300 `/scratch/stefan/7916156/working/3D/300' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=CC=NN2)C1) `REAL250005074185.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005074185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074185/1/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074185 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=CC=NN2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 1, 1, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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: [10, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 10, 10, 10, 21, 21, 46, 46, 46, 46, 10, 10, 10, 10, 6, 1, 10, 10, 46, 46, 46, 10, 10] 46 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 25] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 98 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074185 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=CC=NN2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 1, 1, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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: [1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 10, 1, 1, 1, 6, 6, 29, 29, 29, 29, 1, 2, 2, 2, 3, 10, 1, 1, 29, 29, 29, 1, 1] 46 rigid atoms, others: [0, 1, 2, 32, 11, 12, 13, 20, 26, 27, 31] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30]) total number of confs: 63 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.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: REAL250005074185 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=CC=NN2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 1, 1, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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: [29, 29, 29, 44, 44, 44, 46, 46, 46, 46, 46, 29, 9, 1, 9, 1, 1, 1, 1, 1, 29, 29, 29, 29, 44, 46, 29, 29, 1, 1, 1, 29, 29] 46 rigid atoms, others: [13, 15, 16, 17, 18, 19, 28, 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, 31, 32]) total number of confs: 110 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074185 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074185 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 1: /scratch/stefan/7916156/working/building/REAL250005074185/1.* 0: /scratch/stefan/7916156/working/building/REAL250005074185/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074185 Building REAL250005074186 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074186' /scratch/stefan/7916156/working/building/REAL250005074186 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074186 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074186/0 /scratch/stefan/7916156/working/building/REAL250005074186 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 301) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/301 `/scratch/stefan/7916156/working/3D/301' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSC(C)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074186.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074186/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074186 none CSC(C)C(=O)N1CC(C)(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 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [28, 19, 13, 19, 8, 13, 8, 8, 6, 8, 6, 1, 6, 1, 1, 1, 1, 1, 1, 8, 28, 28, 28, 19, 19, 19, 19, 8, 8, 8, 8, 8, 7, 1, 8, 8] 28 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: 84 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074186 none CSC(C)C(=O)N1CC(C)(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 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [24, 13, 5, 13, 1, 5, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 1, 24, 24, 24, 13, 13, 13, 13, 1, 1, 2, 2, 2, 3, 8, 1, 1] 28 rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 10, 19, 27, 28] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074186 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074186 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074186/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074186 Building REAL250005074187 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074187' /scratch/stefan/7916156/working/building/REAL250005074187 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074187 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074187/0 /scratch/stefan/7916156/working/building/REAL250005074187 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 302) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/302 `/scratch/stefan/7916156/working/3D/302' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(C)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074187.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074187/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074187 none CCOC(C)C(=O)N1CC(C)(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 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [58, 57, 49, 21, 49, 10, 21, 10, 10, 7, 10, 7, 1, 7, 1, 1, 1, 1, 1, 1, 10, 58, 58, 58, 58, 58, 49, 49, 49, 49, 10, 10, 10, 10, 10, 8, 1, 10, 10] 58 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: 204 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074187 none CCOC(C)C(=O)N1CC(C)(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 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [46, 43, 28, 6, 28, 1, 6, 1, 1, 1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 10, 1, 46, 46, 46, 46, 46, 28, 28, 28, 28, 1, 1, 2, 2, 2, 3, 10, 1, 1] 58 rigid atoms, others: [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, 32, 33, 34, 35, 36]) total number of confs: 163 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074187 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074187 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074187/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074187 Building REAL250005074188 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074188' /scratch/stefan/7916156/working/building/REAL250005074188 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074188 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074188/0 /scratch/stefan/7916156/working/building/REAL250005074188 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 303) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/303 `/scratch/stefan/7916156/working/3D/303' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=CNN=C2)C1) `REAL250005074188.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074188.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074188/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074188 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=CNN=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 1, 8, 8, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 13, 13, 13, 26, 26, 33, 33, 33, 33, 13, 13, 13, 13, 7, 1, 13, 13, 33, 33, 33, 13, 13] 33 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 25] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 97 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074188 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=CNN=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 1, 8, 8, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 3, 3, 3, 13, 13, 13, 13, 13, 1, 1, 1, 6, 6, 16, 16, 16, 16, 1, 2, 2, 2, 3, 13, 1, 1, 16, 16, 16, 1, 1] 33 rigid atoms, others: [0, 1, 2, 32, 11, 12, 13, 20, 26, 27, 31] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30]) 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.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: REAL250005074188 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=CNN=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 1, 8, 8, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 34, 34, 34, 44, 44, 44, 44, 44, 26, 10, 1, 10, 1, 1, 1, 1, 1, 26, 26, 26, 26, 34, 44, 26, 26, 1, 1, 1, 26, 26] 44 rigid atoms, others: [13, 15, 16, 17, 18, 19, 28, 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, 31, 32]) total number of confs: 96 number of broken/clashed sets: 5 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074188 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074188 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074188/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074188 Building REAL250005074189 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074189' /scratch/stefan/7916156/working/building/REAL250005074189 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074189 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074189/0 /scratch/stefan/7916156/working/building/REAL250005074189 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 304) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/304 `/scratch/stefan/7916156/working/3D/304' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074189.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074189/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074189 none COCCCC(=O)N1CC(C)(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 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [121, 121, 73, 62, 18, 8, 18, 8, 8, 7, 8, 7, 1, 7, 1, 1, 1, 1, 1, 1, 8, 121, 121, 121, 114, 116, 84, 84, 62, 62, 8, 8, 8, 8, 8, 7, 1, 8, 8] 121 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: 556 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074189 none COCCCC(=O)N1CC(C)(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 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [113, 103, 50, 39, 6, 1, 6, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 1, 113, 113, 113, 94, 96, 62, 62, 39, 39, 1, 1, 2, 2, 2, 3, 8, 1, 1] 121 rigid atoms, others: [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, 32, 33, 34, 35, 36]) total number of confs: 522 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074189 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074189 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074189/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074189 Building REAL250005074190 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074190' /scratch/stefan/7916156/working/building/REAL250005074190 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074190 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074190/0 /scratch/stefan/7916156/working/building/REAL250005074190 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 305) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/305 `/scratch/stefan/7916156/working/3D/305' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=NOC=C2)C1) `REAL250005074190.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074190/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074190 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=NOC=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 8, 12, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [12, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 12, 12, 12, 26, 26, 37, 37, 37, 37, 12, 12, 12, 12, 7, 1, 12, 12, 37, 37, 12, 12] 37 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 25] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31]) total number of confs: 95 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074190 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=NOC=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 8, 12, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 3, 3, 3, 12, 12, 12, 12, 12, 1, 1, 1, 6, 6, 26, 26, 26, 26, 1, 2, 2, 2, 3, 12, 1, 1, 26, 26, 1, 1] 37 rigid atoms, others: [0, 1, 2, 11, 12, 13, 20, 26, 27, 30, 31] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29]) 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.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: REAL250005074190 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=NOC=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 8, 12, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 35, 35, 35, 37, 37, 37, 37, 37, 26, 11, 1, 11, 1, 1, 1, 1, 1, 26, 26, 26, 26, 35, 37, 26, 26, 1, 1, 26, 26] 37 rigid atoms, others: [13, 15, 16, 17, 18, 19, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31]) total number of confs: 84 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074190 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074190 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074190/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074190 Building REAL250005074191 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074191' /scratch/stefan/7916156/working/building/REAL250005074191 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074191 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074191/0 /scratch/stefan/7916156/working/building/REAL250005074191 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 306) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/306 `/scratch/stefan/7916156/working/3D/306' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC=C(C)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074191.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074191/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074191 none CCC=C(C)C(=O)N1CC(C)(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 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [64, 59, 59, 20, 59, 8, 20, 8, 8, 7, 8, 7, 1, 7, 1, 1, 1, 1, 1, 1, 8, 64, 64, 64, 64, 64, 59, 59, 59, 59, 8, 8, 8, 8, 8, 7, 1, 8, 8] 64 rigid atoms, others: [36, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 187 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074191 none CCC=C(C)C(=O)N1CC(C)(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 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [45, 34, 34, 6, 34, 1, 6, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 1, 45, 45, 45, 45, 45, 34, 34, 34, 34, 1, 1, 2, 2, 2, 3, 8, 1, 1] 64 rigid atoms, others: [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, 32, 33, 34, 35, 36]) total number of confs: 153 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074191 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074191 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074191/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074191 Building REAL250005074192 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074192' /scratch/stefan/7916156/working/building/REAL250005074192 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074192 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074192/0 /scratch/stefan/7916156/working/building/REAL250005074192 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 307) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/307 `/scratch/stefan/7916156/working/3D/307' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074192.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074192/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074192 none COC(C)C(=O)N1CC(C)(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 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [29, 27, 16, 27, 8, 16, 8, 8, 6, 8, 6, 1, 6, 1, 1, 1, 1, 1, 1, 8, 29, 29, 29, 27, 27, 27, 27, 8, 8, 8, 8, 8, 7, 1, 8, 8] 29 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: 105 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074192 none COC(C)C(=O)N1CC(C)(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 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [24, 19, 6, 19, 1, 6, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 1, 24, 24, 24, 19, 19, 19, 19, 1, 1, 2, 2, 2, 3, 8, 1, 1] 29 rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 10, 19, 27, 28] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074192 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074192 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074192/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074192 Building REAL250005074193 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074193' /scratch/stefan/7916156/working/building/REAL250005074193 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074193 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074193/0 /scratch/stefan/7916156/working/building/REAL250005074193 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 308) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/308 `/scratch/stefan/7916156/working/3D/308' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)OCC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074193.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074193.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074193/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074193 none CC(C)OCC(=O)N1CC(C)(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 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [147, 132, 147, 83, 26, 11, 26, 11, 11, 8, 11, 8, 1, 8, 1, 1, 1, 1, 1, 1, 11, 147, 147, 147, 147, 147, 147, 147, 83, 83, 11, 11, 11, 11, 11, 8, 1, 11, 11] 147 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: 459 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074193 none CC(C)OCC(=O)N1CC(C)(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 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [118, 91, 118, 42, 6, 1, 6, 1, 1, 1, 1, 1, 3, 3, 3, 11, 11, 11, 11, 11, 1, 118, 118, 118, 118, 118, 118, 118, 42, 42, 1, 1, 2, 2, 2, 3, 11, 1, 1] 147 rigid atoms, others: [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, 32, 33, 34, 35, 36]) total number of confs: 384 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074193 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074193 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074193/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074193 Building REAL250005074194 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074194' /scratch/stefan/7916156/working/building/REAL250005074194 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074194 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074194/0 /scratch/stefan/7916156/working/building/REAL250005074194 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 309) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/309 `/scratch/stefan/7916156/working/3D/309' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOCC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074194.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074194/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074194 none CCCOCC(=O)N1CC(C)(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, 189, 152, 90, 21, 8, 21, 8, 8, 5, 8, 5, 1, 5, 1, 1, 1, 1, 1, 1, 8, 201, 201, 201, 201, 201, 189, 189, 90, 90, 8, 8, 8, 8, 8, 5, 1, 8, 8] 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: 688 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074194 none CCCOCC(=O)N1CC(C)(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: [178, 140, 86, 37, 6, 1, 6, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 1, 178, 178, 178, 178, 178, 140, 140, 37, 37, 1, 1, 2, 2, 2, 3, 8, 1, 1] 201 rigid atoms, others: [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, 32, 33, 34, 35, 36]) total number of confs: 704 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074194 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074194 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074194/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074194 Building REAL250005074195 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074195' /scratch/stefan/7916156/working/building/REAL250005074195 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074195 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074195/0 /scratch/stefan/7916156/working/building/REAL250005074195 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 310) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/310 `/scratch/stefan/7916156/working/3D/310' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2CCOC2)C1) `REAL250005074195.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074195/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074195 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2CCOC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [13, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 13, 13, 13, 27, 27, 44, 44, 44, 44, 13, 13, 13, 13, 7, 1, 13, 13, 44, 44, 44, 44, 44, 44, 44, 13, 13] 44 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 25] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 137 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074195 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2CCOC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 3, 3, 3, 13, 13, 13, 13, 13, 1, 1, 1, 6, 6, 25, 25, 25, 25, 1, 2, 2, 2, 3, 13, 1, 1, 25, 25, 25, 25, 25, 25, 25, 1, 1] 44 rigid atoms, others: [0, 1, 2, 35, 36, 11, 12, 13, 20, 26, 27] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34]) 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.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: REAL250005074195 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2CCOC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [25, 25, 25, 39, 39, 39, 44, 44, 44, 44, 44, 25, 7, 1, 7, 1, 1, 1, 1, 1, 25, 25, 25, 25, 39, 44, 25, 25, 1, 1, 1, 1, 1, 1, 1, 25, 25] 44 rigid atoms, others: [32, 33, 34, 13, 15, 16, 17, 18, 19, 28, 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, 35, 36]) total number of confs: 105 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074195 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074195 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074195/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074195 Building REAL250005074196 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074196' /scratch/stefan/7916156/working/building/REAL250005074196 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074196 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074196/0 /scratch/stefan/7916156/working/building/REAL250005074196 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 311) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/311 `/scratch/stefan/7916156/working/3D/311' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(OC)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074196.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074196.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074196/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074196 none CCC(OC)C(=O)N1CC(C)(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 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [37, 36, 18, 36, 39, 7, 18, 7, 7, 5, 7, 5, 1, 5, 1, 1, 1, 1, 1, 1, 7, 40, 40, 40, 40, 40, 36, 39, 39, 39, 7, 7, 7, 7, 7, 6, 1, 7, 7] 40 rigid atoms, others: [36, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 178 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074196 none CCC(OC)C(=O)N1CC(C)(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 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [25, 23, 6, 23, 32, 1, 6, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 1, 31, 31, 31, 31, 31, 23, 32, 32, 32, 1, 1, 2, 2, 2, 3, 7, 1, 1] 40 rigid atoms, others: [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, 32, 33, 34, 35, 36]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074196 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074196 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074196/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074196 Building REAL250005074197 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074197' /scratch/stefan/7916156/working/building/REAL250005074197 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074197 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074197/0 /scratch/stefan/7916156/working/building/REAL250005074197 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 312) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/312 `/scratch/stefan/7916156/working/3D/312' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)CC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074197.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074197.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074197/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074197 none COC(C)CC(=O)N1CC(C)(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 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [101, 101, 75, 101, 21, 8, 21, 8, 8, 6, 8, 6, 1, 6, 1, 1, 1, 1, 1, 1, 8, 101, 101, 101, 101, 101, 101, 101, 75, 75, 8, 8, 8, 8, 8, 6, 1, 8, 8] 101 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: 405 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074197 none COC(C)CC(=O)N1CC(C)(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 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [78, 72, 39, 72, 6, 1, 6, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 1, 78, 78, 78, 72, 72, 72, 72, 39, 39, 1, 1, 2, 2, 2, 3, 8, 1, 1] 101 rigid atoms, others: [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, 32, 33, 34, 35, 36]) total number of confs: 322 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074197 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074197 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074197/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074197 Building REAL250005074198 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074198' /scratch/stefan/7916156/working/building/REAL250005074198 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074198 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074198/0 /scratch/stefan/7916156/working/building/REAL250005074198 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 313) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/313 `/scratch/stefan/7916156/working/3D/313' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074198.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074198/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074198 none C=CCCC(=O)N1CC(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, 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 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [85, 85, 69, 21, 9, 21, 9, 9, 6, 9, 6, 1, 6, 1, 1, 1, 1, 1, 1, 9, 85, 85, 85, 85, 85, 69, 69, 9, 9, 9, 9, 9, 6, 1, 9, 9] 85 rigid atoms, others: [33, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35]) total number of confs: 345 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074198 none C=CCCC(=O)N1CC(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, 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 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [68, 46, 31, 6, 1, 6, 1, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 1, 68, 68, 68, 46, 46, 31, 31, 1, 1, 2, 2, 2, 3, 9, 1, 1] 85 rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 10, 19, 27, 28] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 280 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074198 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074198 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074198/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074198 Building REAL250005074199 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074199' /scratch/stefan/7916156/working/building/REAL250005074199 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074199 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074199/0 /scratch/stefan/7916156/working/building/REAL250005074199 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 314) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/314 `/scratch/stefan/7916156/working/3D/314' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074199.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074199.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074199/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074199 none CCOCCC(=O)N1CC(C)(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 127 conformations in input total number of sets (complete confs): 127 using faster count positions algorithm for large data unique positions, atoms: [127, 125, 103, 68, 19, 8, 19, 8, 8, 6, 8, 6, 1, 6, 1, 1, 1, 1, 1, 1, 8, 127, 127, 127, 127, 127, 103, 103, 68, 68, 8, 8, 8, 8, 8, 6, 1, 8, 8] 127 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: 487 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074199 none CCOCCC(=O)N1CC(C)(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 127 conformations in input total number of sets (complete confs): 127 using faster count positions algorithm for large data unique positions, atoms: [109, 102, 58, 32, 6, 1, 6, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 1, 110, 110, 110, 109, 109, 58, 58, 32, 32, 1, 1, 2, 2, 2, 3, 8, 1, 1] 127 rigid atoms, others: [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, 32, 33, 34, 35, 36]) total number of confs: 380 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074199 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074199 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074199/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074199 Building REAL250005074200 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074200' /scratch/stefan/7916156/working/building/REAL250005074200 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074200 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074200/0 /scratch/stefan/7916156/working/building/REAL250005074200 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 315) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/315 `/scratch/stefan/7916156/working/3D/315' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(C)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074200.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074200/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074200 none COCC(C)C(=O)N1CC(C)(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 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 43, 19, 43, 9, 19, 9, 9, 7, 9, 7, 1, 7, 1, 1, 1, 1, 1, 1, 9, 55, 55, 55, 55, 55, 43, 43, 43, 43, 9, 9, 9, 9, 9, 8, 1, 9, 9] 55 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: 225 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074200 none COCC(C)C(=O)N1CC(C)(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 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [45, 39, 22, 7, 22, 1, 7, 1, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 1, 45, 45, 45, 39, 39, 22, 22, 22, 22, 1, 1, 2, 2, 2, 3, 9, 1, 1] 55 rigid atoms, others: [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, 32, 33, 34, 35, 36]) total number of confs: 186 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074200 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074200 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074200/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074200 Building REAL250005074201 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074201' /scratch/stefan/7916156/working/building/REAL250005074201 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074201 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074201/0 /scratch/stefan/7916156/working/building/REAL250005074201 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 316) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/316 `/scratch/stefan/7916156/working/3D/316' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCOCC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074201.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074201/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074201 none C=CCOCC(=O)N1CC(C)(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 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [123, 123, 88, 42, 16, 10, 16, 10, 10, 7, 10, 7, 1, 7, 1, 1, 1, 1, 1, 1, 10, 123, 123, 123, 123, 123, 42, 42, 10, 10, 10, 10, 10, 7, 1, 10, 10] 123 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: 400 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074201 none C=CCOCC(=O)N1CC(C)(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 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [97, 79, 41, 15, 2, 1, 2, 1, 1, 1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 10, 1, 97, 97, 97, 79, 79, 15, 15, 1, 1, 2, 2, 2, 3, 10, 1, 1] 123 rigid atoms, others: [35, 36, 5, 7, 8, 9, 10, 11, 20, 28, 29] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34]) total number of confs: 356 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074201 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074201 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074201/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074201 Building REAL250005074202 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074202' /scratch/stefan/7916156/working/building/REAL250005074202 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074202 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074202/0 /scratch/stefan/7916156/working/building/REAL250005074202 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 317) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/317 `/scratch/stefan/7916156/working/3D/317' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=COC=N2)C1) `REAL250005074202.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074202/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074202 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=COC=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 1, 12, 1, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [10, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 10, 10, 10, 22, 22, 32, 32, 32, 32, 10, 10, 10, 10, 7, 1, 10, 10, 32, 32, 10, 10] 32 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 25] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31]) total number of confs: 81 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074202 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=COC=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 1, 12, 1, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 10, 1, 1, 1, 6, 6, 20, 20, 20, 20, 1, 2, 2, 2, 3, 10, 1, 1, 20, 20, 1, 1] 32 rigid atoms, others: [0, 1, 2, 11, 12, 13, 20, 26, 27, 30, 31] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074202 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=COC=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 1, 12, 1, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [20, 20, 20, 29, 29, 29, 32, 32, 32, 32, 32, 20, 12, 1, 12, 1, 1, 1, 1, 1, 20, 20, 20, 20, 29, 32, 20, 20, 1, 1, 20, 20] 32 rigid atoms, others: [13, 15, 16, 17, 18, 19, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31]) total number of confs: 79 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074202 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074202 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074202/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074202 Building REAL250005074203 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074203' /scratch/stefan/7916156/working/building/REAL250005074203 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074203 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074203/0 /scratch/stefan/7916156/working/building/REAL250005074203 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 318) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/318 `/scratch/stefan/7916156/working/3D/318' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C#N)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074203.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074203/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074203 none CC(C#N)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.1', 'N.1', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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, 15, 21, 21, 8, 15, 8, 8, 6, 8, 6, 1, 6, 1, 1, 1, 1, 1, 1, 8, 21, 21, 21, 21, 8, 8, 8, 8, 8, 7, 1, 8, 8] 21 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32]) total number of confs: 76 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074203 none CC(C#N)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.1', 'N.1', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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: [15, 5, 15, 15, 1, 5, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 1, 15, 15, 15, 15, 1, 1, 2, 2, 2, 3, 8, 1, 1] 21 rigid atoms, others: [32, 4, 6, 7, 8, 9, 10, 19, 24, 25, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 26, 27, 28, 29, 30]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074203 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074203 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074203/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074203 Building REAL250005074204 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074204' /scratch/stefan/7916156/working/building/REAL250005074204 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074204 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074204/0 /scratch/stefan/7916156/working/building/REAL250005074204 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 319) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/319 `/scratch/stefan/7916156/working/3D/319' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(C)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074204.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074204/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074204 none CCCC(C)C(=O)N1CC(C)(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 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [57, 54, 45, 24, 45, 12, 24, 12, 12, 9, 12, 9, 1, 9, 1, 1, 1, 1, 1, 1, 12, 57, 57, 57, 56, 57, 55, 55, 45, 45, 45, 45, 12, 12, 12, 12, 12, 9, 1, 12, 12] 57 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: 225 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074204 none CCCC(C)C(=O)N1CC(C)(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 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [42, 37, 22, 7, 22, 1, 7, 1, 1, 1, 1, 1, 3, 3, 3, 12, 12, 12, 12, 12, 1, 42, 42, 42, 41, 42, 38, 38, 22, 22, 22, 22, 1, 1, 2, 2, 2, 3, 12, 1, 1] 57 rigid atoms, others: [32, 33, 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, 34, 35, 36, 37, 38]) total number of confs: 213 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074204 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074204 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074204/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074204 Building REAL250005074205 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074205' /scratch/stefan/7916156/working/building/REAL250005074205 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074205 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074205/0 /scratch/stefan/7916156/working/building/REAL250005074205 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 320) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/320 `/scratch/stefan/7916156/working/3D/320' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)CCC2CC2)C1) `REAL250005074205.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074205/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074205 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)CCC2CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 198 conformations in input total number of sets (complete confs): 198 using faster count positions algorithm for large data unique positions, atoms: [15, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 15, 15, 15, 40, 40, 129, 143, 198, 198, 15, 15, 15, 15, 9, 1, 15, 15, 129, 129, 147, 147, 198, 198, 198, 198, 198, 15, 15] 198 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 25] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 786 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074205 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)CCC2CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 198 conformations in input total number of sets (complete confs): 198 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 3, 3, 3, 15, 15, 15, 15, 15, 1, 1, 1, 6, 6, 43, 58, 109, 109, 1, 2, 2, 2, 3, 15, 1, 1, 43, 43, 73, 73, 109, 109, 109, 109, 109, 1, 1] 198 rigid atoms, others: [0, 1, 2, 37, 38, 11, 12, 13, 20, 26, 27] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36]) 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.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: REAL250005074205 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)CCC2CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 198 conformations in input total number of sets (complete confs): 198 using faster count positions algorithm for large data unique positions, atoms: [109, 109, 109, 174, 174, 174, 198, 198, 198, 198, 198, 109, 40, 7, 40, 3, 1, 1, 1, 1, 109, 109, 109, 109, 174, 198, 109, 109, 7, 7, 3, 3, 1, 1, 1, 1, 1, 109, 109] 198 rigid atoms, others: [32, 33, 34, 35, 36, 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, 37, 38]) total number of confs: 513 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074205 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074205 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074205/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074205 Building REAL250005074206 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074206' /scratch/stefan/7916156/working/building/REAL250005074206 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074206 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074206/0 /scratch/stefan/7916156/working/building/REAL250005074206 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 321) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/321 `/scratch/stefan/7916156/working/3D/321' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2CC=CC2)C1) `REAL250005074206.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074206/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074206 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2CC=CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 1, 1, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 13, 13, 13, 26, 26, 46, 46, 46, 46, 13, 13, 13, 13, 7, 1, 13, 13, 46, 46, 46, 46, 46, 46, 46, 13, 13] 46 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 25] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 147 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074206 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2CC=CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 1, 1, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 3, 3, 3, 13, 13, 13, 13, 13, 1, 1, 1, 6, 6, 31, 31, 31, 31, 1, 2, 2, 2, 3, 13, 1, 1, 31, 31, 31, 31, 31, 31, 31, 1, 1] 46 rigid atoms, others: [0, 1, 2, 35, 36, 11, 12, 13, 20, 26, 27] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 99 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.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: REAL250005074206 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2CC=CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 1, 1, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 39, 39, 39, 46, 46, 46, 46, 46, 31, 9, 1, 9, 1, 1, 1, 1, 1, 31, 31, 31, 31, 39, 46, 31, 31, 1, 1, 1, 1, 1, 1, 1, 31, 31] 46 rigid atoms, others: [32, 33, 34, 13, 15, 16, 17, 18, 19, 28, 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, 35, 36]) total number of confs: 95 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074206 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074206 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074206/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074206 Building REAL250005074207 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074207' /scratch/stefan/7916156/working/building/REAL250005074207 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074207 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074207/0 /scratch/stefan/7916156/working/building/REAL250005074207 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 322) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/322 `/scratch/stefan/7916156/working/3D/322' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)CC2CCC2)C1) `REAL250005074207.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074207/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074207 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)CC2CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 95 conformations in input total number of sets (complete confs): 95 using faster count positions algorithm for large data unique positions, atoms: [14, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 14, 14, 14, 35, 35, 70, 95, 95, 95, 14, 14, 14, 14, 8, 1, 14, 14, 70, 70, 95, 95, 95, 95, 95, 95, 95, 14, 14] 95 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 25] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 370 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074207 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)CC2CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 95 conformations in input total number of sets (complete confs): 95 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 3, 3, 3, 14, 14, 14, 14, 14, 1, 1, 1, 6, 6, 36, 59, 59, 59, 1, 2, 2, 2, 3, 14, 1, 1, 36, 36, 59, 59, 59, 59, 59, 59, 59, 1, 1] 95 rigid atoms, others: [0, 1, 2, 37, 38, 11, 12, 13, 20, 26, 27] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 230 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074207 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)CC2CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 95 conformations in input total number of sets (complete confs): 95 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 59, 81, 81, 81, 95, 95, 95, 95, 95, 59, 30, 7, 30, 1, 1, 1, 1, 1, 59, 59, 59, 59, 81, 95, 59, 59, 7, 7, 1, 1, 1, 1, 1, 1, 1, 59, 59] 95 rigid atoms, others: [32, 33, 34, 35, 36, 15, 16, 17, 18, 19, 30, 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, 37, 38]) total number of confs: 242 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074207 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074207 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074207/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074207 Building REAL250005074208 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074208' /scratch/stefan/7916156/working/building/REAL250005074208 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074208 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074208/0 /scratch/stefan/7916156/working/building/REAL250005074208 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 323) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/323 `/scratch/stefan/7916156/working/3D/323' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1)C1CC1) `REAL250005074208.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074208.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074208/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074208 none CC(C(=O)N1CC(C)(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 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [30, 15, 7, 15, 7, 6, 5, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 30, 30, 30, 30, 30, 30, 30, 7, 7, 7, 7, 7, 5, 1, 6, 6, 30, 30, 30, 30, 30] 30 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: 127 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074208 none CC(C(=O)N1CC(C)(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 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [22, 7, 1, 7, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 1, 22, 23, 23, 22, 22, 22, 22, 1, 1, 2, 2, 2, 2, 6, 1, 1, 23, 23, 23, 23, 23] 30 rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 17, 25, 26] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38]) total number of confs: 97 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.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: REAL250005074208 none CC(C(=O)N1CC(C)(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 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 9, 9, 23, 23, 23, 23, 27, 27, 27, 30, 30, 30, 30, 30, 23, 1, 1, 1, 4, 4, 4, 3, 23, 23, 23, 23, 23, 27, 30, 23, 23, 1, 1, 1, 1, 1] 30 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: 75 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074208 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074208 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074208/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074208 Building REAL250005074209 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074209' /scratch/stefan/7916156/working/building/REAL250005074209 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074209 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074209/0 /scratch/stefan/7916156/working/building/REAL250005074209 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 324) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/324 `/scratch/stefan/7916156/working/3D/324' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=C(C)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074209.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074209/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074209 none CC=C(C)C(=O)N1CC(C)(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 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 24, 36, 11, 24, 11, 11, 8, 11, 8, 1, 8, 1, 1, 1, 1, 1, 1, 11, 36, 36, 36, 36, 36, 36, 36, 11, 11, 11, 11, 11, 8, 1, 11, 11] 36 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: 111 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074209 none CC=C(C)C(=O)N1CC(C)(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 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 7, 23, 1, 7, 1, 1, 1, 1, 1, 3, 3, 3, 11, 11, 11, 11, 11, 1, 23, 23, 23, 23, 23, 23, 23, 1, 1, 2, 2, 2, 3, 11, 1, 1] 36 rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 10, 19, 27, 28] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074209 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074209 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074209/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074209 Building REAL250005074210 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074210' /scratch/stefan/7916156/working/building/REAL250005074210 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074210 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074210/0 /scratch/stefan/7916156/working/building/REAL250005074210 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 325) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/325 `/scratch/stefan/7916156/working/3D/325' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC(C(=O)N2CC(C)(NC(=O)C3=CC(=O)[N-]O3)C2)C1) `REAL250005074210.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074210/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074210 none CC1CC(C(=O)N2CC(C)(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 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 6, 1, 6, 1, 1, 1, 1, 1, 2, 2, 2, 13, 13, 13, 13, 13, 1, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 2, 2, 2, 2, 13, 1, 1, 20, 20] 33 rigid atoms, others: [35, 4, 6, 7, 8, 9, 10, 19, 36, 28, 29] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 37, 38]) total number of confs: 74 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074210 none CC1CC(C(=O)N2CC(C)(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 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 8, 8, 20, 20, 20, 20, 27, 27, 27, 33, 33, 33, 33, 33, 20, 1, 2, 2, 2, 1, 1, 1, 1, 20, 20, 20, 20, 20, 27, 33, 20, 20, 1, 1] 33 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: 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.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: REAL250005074210 none CC1CC(C(=O)N2CC(C)(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 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 27, 13, 27, 13, 13, 10, 13, 10, 1, 10, 1, 1, 1, 1, 1, 1, 13, 33, 33, 33, 33, 33, 33, 33, 33, 13, 13, 14, 14, 14, 10, 1, 13, 13, 33, 33] 33 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: 97 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074210 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074210 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074210/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074210 Building REAL250005074211 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074211' /scratch/stefan/7916156/working/building/REAL250005074211 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074211 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074211/0 /scratch/stefan/7916156/working/building/REAL250005074211 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 326) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/326 `/scratch/stefan/7916156/working/3D/326' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C=C2CCC2)C1) `REAL250005074211.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074211/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074211 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C=C2CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 12, 12, 12, 22, 22, 50, 50, 50, 50, 12, 12, 12, 12, 7, 1, 12, 12, 50, 50, 50, 50, 50, 50, 50, 12, 12] 50 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 25] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 145 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074211 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C=C2CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 3, 3, 3, 12, 12, 12, 12, 12, 1, 1, 1, 6, 6, 26, 26, 26, 26, 1, 2, 2, 2, 3, 12, 1, 1, 26, 26, 26, 26, 26, 26, 26, 1, 1] 50 rigid atoms, others: [0, 1, 2, 35, 36, 11, 12, 13, 20, 26, 27] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 88 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.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: REAL250005074211 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C=C2CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 44, 44, 44, 50, 50, 50, 50, 50, 26, 9, 1, 9, 1, 1, 1, 1, 1, 26, 27, 27, 27, 44, 50, 26, 26, 1, 1, 1, 1, 1, 1, 1, 26, 26] 50 rigid atoms, others: [32, 33, 34, 13, 15, 16, 17, 18, 19, 28, 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, 35, 36]) total number of confs: 132 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074211 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074211 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074211/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074211 Building REAL250005074212 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074212' /scratch/stefan/7916156/working/building/REAL250005074212 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074212 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074212/0 /scratch/stefan/7916156/working/building/REAL250005074212 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 327) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/327 `/scratch/stefan/7916156/working/3D/327' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)=C(F)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074212.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074212/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074212 none CC(C)=C(F)C(=O)N1CC(C)(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 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 12, 19, 6, 12, 6, 6, 4, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 6, 19, 19, 19, 19, 19, 19, 6, 6, 6, 6, 6, 4, 1, 6, 6] 19 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: 59 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074212 none CC(C)=C(F)C(=O)N1CC(C)(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 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 6, 13, 1, 6, 1, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 6, 1, 13, 13, 13, 13, 13, 13, 1, 1, 2, 2, 2, 3, 6, 1, 1] 19 rigid atoms, others: [34, 35, 5, 7, 8, 9, 10, 11, 20, 27, 28] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074212 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074212 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074212/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074212 Building REAL250005074213 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074213' /scratch/stefan/7916156/working/building/REAL250005074213 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074213 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074213/0 /scratch/stefan/7916156/working/building/REAL250005074213 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 328) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/328 `/scratch/stefan/7916156/working/3D/328' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=CCCC2)C1) `REAL250005074213.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074213/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074213 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=CCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [16, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 16, 16, 16, 31, 31, 41, 41, 41, 41, 16, 16, 16, 16, 9, 1, 16, 16, 41, 41, 41, 41, 41, 41, 41, 16, 16] 41 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 25] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 113 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074213 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=CCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 3, 16, 16, 16, 16, 16, 1, 1, 1, 7, 7, 19, 19, 19, 19, 1, 2, 2, 2, 3, 16, 1, 1, 19, 19, 19, 19, 19, 19, 19, 1, 1] 41 rigid atoms, others: [0, 1, 2, 35, 36, 11, 12, 13, 20, 26, 27] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 60 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.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: REAL250005074213 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=CCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 33, 33, 33, 41, 41, 41, 41, 41, 19, 9, 1, 9, 1, 1, 1, 1, 1, 19, 19, 19, 19, 33, 41, 19, 19, 1, 1, 1, 1, 1, 1, 1, 19, 19] 41 rigid atoms, others: [32, 33, 34, 13, 15, 16, 17, 18, 19, 28, 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, 35, 36]) total number of confs: 104 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074213 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074213 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074213/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074213 Building REAL250005074214 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074214' /scratch/stefan/7916156/working/building/REAL250005074214 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074214 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074214/0 /scratch/stefan/7916156/working/building/REAL250005074214 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 329) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/329 `/scratch/stefan/7916156/working/3D/329' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CC1C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074214.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074214/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074214 none CC1(C)CC1C(=O)N1CC(C)(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 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 6, 1, 6, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 2, 2, 2, 2, 7, 1, 1] 23 rigid atoms, others: [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, 32, 33, 34, 35, 36]) total number of confs: 54 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074214 none CC1(C)CC1C(=O)N1CC(C)(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 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 15, 15, 15, 15, 20, 20, 20, 23, 23, 23, 23, 23, 15, 2, 2, 2, 2, 2, 2, 1, 1, 1, 15, 15, 15, 15, 15, 20, 23, 15, 15] 23 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: 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.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: REAL250005074214 none CC1(C)CC1C(=O)N1CC(C)(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 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 13, 7, 13, 7, 7, 5, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 7, 23, 23, 23, 23, 23, 23, 23, 23, 23, 7, 7, 7, 7, 7, 6, 1, 7, 7] 23 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: 74 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074214 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074214 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074214/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074214 Building REAL250005074215 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074215' /scratch/stefan/7916156/working/building/REAL250005074215 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074215 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074215/0 /scratch/stefan/7916156/working/building/REAL250005074215 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 330) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/330 `/scratch/stefan/7916156/working/3D/330' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)C[C@@H]1C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074215.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074215/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074215 none CC1(C)C[C@@H]1C(=O)N1CC(C)(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 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 6, 15, 1, 6, 1, 1, 1, 1, 1, 2, 2, 2, 7, 6, 7, 6, 6, 1, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 2, 2, 2, 2, 7, 1, 1] 23 rigid atoms, others: [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, 32, 33, 34, 35, 36]) total number of confs: 56 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074215 none CC1(C)C[C@@H]1C(=O)N1CC(C)(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 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 7, 15, 15, 15, 15, 20, 20, 20, 23, 23, 23, 23, 23, 15, 2, 2, 2, 2, 2, 2, 1, 1, 15, 15, 15, 15, 15, 20, 23, 15, 15] 23 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 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.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: REAL250005074215 none CC1(C)C[C@@H]1C(=O)N1CC(C)(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 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 13, 23, 7, 13, 7, 7, 5, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 7, 23, 23, 23, 23, 23, 23, 23, 23, 7, 7, 7, 7, 7, 6, 1, 7, 7] 23 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: 74 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074215 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074215 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074215/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074215 Building REAL250005074216 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074216' /scratch/stefan/7916156/working/building/REAL250005074216 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074216 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074216/0 /scratch/stefan/7916156/working/building/REAL250005074216 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 331) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/331 `/scratch/stefan/7916156/working/3D/331' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)[C@@H]2CCCO2)C1) `REAL250005074216.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074216/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074216 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)[C@@H]2CCCO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [13, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 13, 13, 13, 30, 30, 56, 56, 56, 56, 56, 13, 13, 13, 13, 6, 1, 13, 13, 56, 56, 56, 56, 56, 56, 13, 13] 56 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 26] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 171 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074216 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)[C@@H]2CCCO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 3, 3, 3, 13, 13, 13, 13, 13, 1, 1, 1, 6, 6, 32, 32, 32, 32, 32, 1, 2, 2, 2, 3, 13, 1, 1, 32, 32, 32, 32, 32, 32, 1, 1] 56 rigid atoms, others: [0, 1, 2, 35, 36, 11, 12, 13, 21, 27, 28] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074216 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)[C@@H]2CCCO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 32, 46, 46, 46, 56, 56, 56, 56, 56, 32, 10, 1, 10, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 46, 56, 32, 32, 1, 1, 1, 1, 1, 1, 32, 32] 56 rigid atoms, others: [32, 33, 34, 13, 15, 16, 17, 18, 19, 20, 29, 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, 35, 36]) total number of confs: 125 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074216 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074216 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074216/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074216 Building REAL250005074217 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074217' /scratch/stefan/7916156/working/building/REAL250005074217 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074217 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074217/0 /scratch/stefan/7916156/working/building/REAL250005074217 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 332) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/332 `/scratch/stefan/7916156/working/3D/332' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)CC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074217.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074217/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074217 none CCC(C)CC(=O)N1CC(C)(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 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [123, 113, 81, 112, 23, 11, 23, 11, 11, 8, 11, 8, 1, 8, 1, 1, 1, 1, 1, 1, 11, 123, 123, 123, 123, 123, 113, 113, 113, 113, 81, 81, 11, 11, 11, 11, 11, 8, 1, 11, 11] 123 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: 532 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074217 none CCC(C)CC(=O)N1CC(C)(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 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [97, 75, 39, 74, 6, 1, 6, 1, 1, 1, 1, 1, 3, 3, 3, 11, 11, 11, 11, 11, 1, 97, 97, 97, 97, 97, 75, 75, 75, 75, 39, 39, 1, 1, 2, 2, 2, 3, 11, 1, 1] 123 rigid atoms, others: [32, 33, 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, 34, 35, 36, 37, 38]) total number of confs: 460 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074217 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074217 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074217/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074217 Building REAL250005074218 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074218' /scratch/stefan/7916156/working/building/REAL250005074218 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074218 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074218/0 /scratch/stefan/7916156/working/building/REAL250005074218 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 333) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/333 `/scratch/stefan/7916156/working/3D/333' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCCC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074218.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074218/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074218 none C#CCCCC(=O)N1CC(C)(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, 117, 108, 26, 11, 26, 11, 11, 8, 11, 8, 1, 8, 1, 1, 1, 1, 1, 1, 11, 201, 191, 194, 135, 135, 108, 108, 11, 11, 11, 11, 11, 8, 1, 11, 11] 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: 929 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074218 none C#CCCCC(=O)N1CC(C)(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: [139, 139, 64, 47, 6, 1, 6, 1, 1, 1, 1, 1, 3, 3, 3, 11, 11, 11, 11, 11, 1, 139, 123, 130, 82, 82, 47, 47, 1, 1, 2, 2, 2, 3, 11, 1, 1] 201 rigid atoms, others: [35, 36, 5, 7, 8, 9, 10, 11, 20, 28, 29] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34]) total number of confs: 686 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074218 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074218 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074218/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074218 Building REAL250005074219 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074219' /scratch/stefan/7916156/working/building/REAL250005074219 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074219 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074219/0 /scratch/stefan/7916156/working/building/REAL250005074219 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 334) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/334 `/scratch/stefan/7916156/working/3D/334' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(O)CC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074219.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074219/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074219 none CC(C)(O)CC(=O)N1CC(C)(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 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [21, 15, 21, 21, 5, 3, 5, 3, 3, 2, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 21, 21, 21, 21, 21, 21, 63, 15, 15, 3, 3, 3, 3, 3, 2, 1, 3, 3] 63 rigid atoms, others: [36, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 150 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074219 none CC(C)(O)CC(=O)N1CC(C)(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 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [21, 13, 21, 21, 3, 1, 3, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 3, 1, 21, 21, 21, 21, 21, 21, 63, 13, 13, 1, 1, 2, 2, 2, 2, 3, 1, 1] 63 rigid atoms, others: [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, 32, 33, 34, 35, 36]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074219 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074219 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074219/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074219 Building REAL250005074220 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074220' /scratch/stefan/7916156/working/building/REAL250005074220 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074220 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074220/0 /scratch/stefan/7916156/working/building/REAL250005074220 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 335) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/335 `/scratch/stefan/7916156/working/3D/335' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](O)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074220.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074220.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074220/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074220 none CC(C)[C@@H](O)C(=O)N1CC(C)(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 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [32, 28, 32, 15, 28, 28, 8, 15, 8, 8, 6, 7, 6, 1, 6, 1, 1, 1, 1, 1, 1, 7, 32, 32, 32, 32, 32, 32, 32, 84, 8, 8, 8, 8, 8, 6, 1, 7, 7] 96 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: 216 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074220 none CC(C)[C@@H](O)C(=O)N1CC(C)(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 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [26, 20, 25, 7, 20, 20, 1, 7, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 1, 26, 26, 26, 26, 26, 26, 26, 60, 1, 1, 2, 2, 2, 2, 7, 1, 1] 96 rigid atoms, others: [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, 32, 33, 34, 35, 36]) total number of confs: 187 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074220 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074220 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074220/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074220 Building REAL250005074221 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074221' /scratch/stefan/7916156/working/building/REAL250005074221 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074221 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074221/0 /scratch/stefan/7916156/working/building/REAL250005074221 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 336) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/336 `/scratch/stefan/7916156/working/3D/336' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)=CC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074221.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074221.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074221/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074221 none CCC(C)=CC(=O)N1CC(C)(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 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [55, 34, 34, 34, 14, 6, 14, 6, 6, 4, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 6, 55, 55, 55, 55, 55, 34, 34, 34, 34, 6, 6, 6, 6, 6, 4, 1, 6, 6] 55 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: 225 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074221 none CCC(C)=CC(=O)N1CC(C)(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 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [36, 24, 24, 24, 6, 1, 6, 1, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 6, 1, 36, 36, 36, 36, 36, 24, 24, 24, 24, 1, 1, 2, 2, 2, 3, 6, 1, 1] 55 rigid atoms, others: [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, 32, 33, 34, 35, 36]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074221 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074221 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074221/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074221 Building REAL250005074222 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074222' /scratch/stefan/7916156/working/building/REAL250005074222 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074222 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074222/0 /scratch/stefan/7916156/working/building/REAL250005074222 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 337) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/337 `/scratch/stefan/7916156/working/3D/337' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C#CC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074222.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074222.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074222/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074222 none CC(C)C#CC(=O)N1CC(C)(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 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 12, 5, 12, 5, 5, 3, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 12, 12, 12, 12, 12, 12, 12, 5, 5, 5, 5, 5, 4, 1, 5, 5] 12 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: 33 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074222 none CC(C)C#CC(=O)N1CC(C)(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 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 5, 1, 7, 7, 7, 6, 6, 6, 6, 1, 1, 2, 2, 2, 3, 5, 1, 1] 12 rigid atoms, others: [35, 36, 5, 7, 8, 9, 10, 11, 20, 28, 29] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34]) total number of confs: 34 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074222 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074222 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074222/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074222 Building REAL250005074223 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074223' /scratch/stefan/7916156/working/building/REAL250005074223 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074223 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074223/0 /scratch/stefan/7916156/working/building/REAL250005074223 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 338) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/338 `/scratch/stefan/7916156/working/3D/338' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C#CC2CC2)C1) `REAL250005074223.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074223/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074223 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C#CC2CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 6, 6, 6, 16, 16, 16, 16, 16, 16, 6, 6, 6, 6, 4, 1, 6, 6, 16, 16, 16, 16, 16, 6, 6] 16 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 25] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 43 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074223 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C#CC2CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 6, 1, 1, 1, 6, 6, 6, 6, 6, 6, 1, 2, 2, 2, 3, 6, 1, 1, 6, 6, 6, 6, 6, 1, 1] 16 rigid atoms, others: [0, 1, 2, 34, 33, 11, 12, 13, 20, 26, 27] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32]) total number of confs: 30 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074223 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C#CC2CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 13, 13, 13, 16, 16, 16, 16, 16, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 13, 16, 6, 6, 1, 1, 1, 1, 1, 6, 6] 16 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34]) total number of confs: 44 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074223 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074223 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074223/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074223 Building REAL250005074224 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074224' /scratch/stefan/7916156/working/building/REAL250005074224 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074224 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074224/0 /scratch/stefan/7916156/working/building/REAL250005074224 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 339) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/339 `/scratch/stefan/7916156/working/3D/339' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074224.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074224.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074224/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074224 none CCC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [18, 12, 10, 12, 10, 10, 7, 10, 7, 1, 7, 1, 1, 1, 1, 1, 1, 10, 18, 18, 18, 18, 18, 10, 10, 10, 10, 10, 7, 1, 10, 10] 18 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: 69 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074224 none CCC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [8, 3, 1, 3, 1, 1, 1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 10, 1, 9, 9, 9, 8, 8, 1, 1, 2, 2, 2, 3, 10, 1, 1] 18 rigid atoms, others: [2, 4, 5, 6, 7, 8, 17, 23, 24, 30, 31] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074224 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074224 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074224/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074224 Building REAL250005074225 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074225' /scratch/stefan/7916156/working/building/REAL250005074225 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074225 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074225/0 /scratch/stefan/7916156/working/building/REAL250005074225 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 340) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/340 `/scratch/stefan/7916156/working/3D/340' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074225.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074225/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074225 none COCCC(=O)N1CC(C)(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 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 51, 18, 8, 18, 8, 8, 6, 8, 6, 1, 6, 1, 1, 1, 1, 1, 1, 8, 67, 67, 67, 67, 67, 51, 51, 8, 8, 8, 8, 8, 6, 1, 8, 8] 67 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: 280 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074225 none COCCC(=O)N1CC(C)(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 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [57, 43, 26, 6, 1, 6, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 1, 57, 57, 57, 43, 43, 26, 26, 1, 1, 2, 2, 2, 3, 8, 1, 1] 67 rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 10, 19, 27, 28] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074225 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074225 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074225/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074225 Building REAL250005074226 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074226' /scratch/stefan/7916156/working/building/REAL250005074226 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074226 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074226/0 /scratch/stefan/7916156/working/building/REAL250005074226 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 341) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/341 `/scratch/stefan/7916156/working/3D/341' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2CC2)C1) `REAL250005074226.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074226/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074226 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [12, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 12, 12, 12, 19, 19, 28, 28, 12, 12, 12, 12, 8, 1, 12, 12, 28, 28, 28, 28, 28, 12, 12] 28 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 23] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 97 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074226 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 3, 3, 3, 12, 12, 12, 12, 12, 1, 1, 1, 6, 6, 14, 14, 1, 2, 2, 2, 3, 12, 1, 1, 14, 14, 14, 14, 14, 1, 1] 28 rigid atoms, others: [0, 1, 2, 32, 11, 12, 13, 18, 24, 25, 31] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30]) 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.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: REAL250005074226 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 20, 20, 20, 28, 28, 28, 28, 28, 14, 8, 1, 8, 1, 1, 1, 14, 14, 14, 14, 20, 28, 14, 14, 1, 1, 1, 1, 1, 14, 14] 28 rigid atoms, others: [13, 15, 16, 17, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 31, 32]) total number of confs: 68 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074226 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074226 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074226/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074226 Building REAL250005074227 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074227' /scratch/stefan/7916156/working/building/REAL250005074227 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074227 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074227/0 /scratch/stefan/7916156/working/building/REAL250005074227 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 342) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/342 `/scratch/stefan/7916156/working/3D/342' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2CCC2)C1) `REAL250005074227.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074227/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074227 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [19, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 19, 19, 19, 34, 34, 38, 38, 38, 19, 19, 19, 19, 11, 1, 19, 19, 38, 38, 38, 38, 38, 38, 38, 19, 19] 38 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 24] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 121 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074227 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 3, 3, 3, 19, 19, 19, 19, 19, 1, 1, 1, 4, 4, 16, 16, 16, 1, 2, 2, 2, 3, 19, 1, 1, 16, 16, 16, 16, 16, 16, 16, 1, 1] 38 rigid atoms, others: [0, 1, 2, 34, 35, 11, 12, 13, 19, 25, 26] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074227 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 28, 28, 28, 38, 38, 38, 38, 38, 16, 8, 1, 8, 1, 1, 1, 1, 16, 16, 16, 16, 28, 38, 16, 16, 1, 1, 1, 1, 1, 1, 1, 16, 16] 38 rigid atoms, others: [32, 33, 13, 15, 16, 17, 18, 27, 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, 34, 35]) total number of confs: 95 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074227 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074227 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074227/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074227 Building REAL250005074228 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074228' /scratch/stefan/7916156/working/building/REAL250005074228 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074228 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074228/0 /scratch/stefan/7916156/working/building/REAL250005074228 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 343) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/343 `/scratch/stefan/7916156/working/3D/343' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2CCCC2)C1) `REAL250005074228.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074228.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074228/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074228 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2CCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 12, 12, 12, 26, 26, 45, 45, 45, 45, 12, 12, 12, 12, 7, 1, 12, 12, 45, 45, 45, 45, 45, 45, 45, 45, 45, 12, 12] 45 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 25] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 145 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074228 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2CCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 3, 3, 3, 12, 12, 12, 12, 12, 1, 1, 1, 6, 6, 24, 24, 24, 24, 1, 2, 2, 2, 3, 12, 1, 1, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1] 45 rigid atoms, others: [0, 1, 2, 37, 38, 11, 12, 13, 20, 26, 27] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 84 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.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: REAL250005074228 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2CCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 36, 36, 36, 45, 45, 45, 45, 45, 24, 8, 1, 8, 1, 1, 1, 1, 1, 24, 24, 24, 24, 36, 45, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24] 45 rigid atoms, others: [32, 33, 34, 35, 36, 13, 15, 16, 17, 18, 19, 28, 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, 37, 38]) total number of confs: 105 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074228 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074228 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074228/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074228 Building REAL250005074229 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074229' /scratch/stefan/7916156/working/building/REAL250005074229 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074229 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074229/0 /scratch/stefan/7916156/working/building/REAL250005074229 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 344) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/344 `/scratch/stefan/7916156/working/3D/344' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCCC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074229.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074229/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074229 none C=CCCCC(=O)N1CC(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, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 128, 102, 20, 8, 20, 8, 8, 7, 8, 7, 1, 7, 1, 1, 1, 1, 1, 1, 8, 201, 201, 201, 190, 193, 146, 146, 102, 102, 8, 8, 8, 8, 8, 7, 1, 8, 8] 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: 918 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074229 none C=CCCCC(=O)N1CC(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, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [174, 138, 66, 45, 6, 1, 6, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 1, 174, 174, 174, 127, 128, 81, 81, 45, 45, 1, 1, 2, 2, 2, 3, 8, 1, 1] 201 rigid atoms, others: [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, 32, 33, 34, 35, 36]) total number of confs: 805 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074229 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074229 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074229/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074229 Building REAL250005074230 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074230' /scratch/stefan/7916156/working/building/REAL250005074230 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074230 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074230/0 /scratch/stefan/7916156/working/building/REAL250005074230 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 345) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/345 `/scratch/stefan/7916156/working/3D/345' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074230.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074230/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074230 none CCC(C)(C)C(=O)N1CC(C)(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 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [43, 35, 20, 35, 35, 9, 20, 9, 9, 6, 9, 6, 1, 6, 1, 1, 1, 1, 1, 1, 9, 43, 43, 43, 43, 43, 35, 35, 35, 35, 35, 35, 9, 9, 9, 9, 9, 6, 1, 9, 9] 43 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: 179 number of broken/clashed sets: 42 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074230 none CCC(C)(C)C(=O)N1CC(C)(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 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [30, 17, 7, 17, 17, 1, 7, 1, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 1, 30, 30, 30, 30, 30, 17, 17, 17, 17, 17, 17, 1, 1, 2, 2, 2, 3, 9, 1, 1] 43 rigid atoms, others: [32, 33, 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, 34, 35, 36, 37, 38]) total number of confs: 155 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074230 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074230 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074230/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074230 Building REAL250005074231 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074231' /scratch/stefan/7916156/working/building/REAL250005074231 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074231 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074231/0 /scratch/stefan/7916156/working/building/REAL250005074231 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 346) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/346 `/scratch/stefan/7916156/working/3D/346' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C(N)=O)C1) `REAL250005074231.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074231/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074231 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 8, 11, 5, 7, 7, 7, 6, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 12, 12, 12, 22, 22, 29, 29, 12, 12, 12, 12, 6, 1, 12, 12, 29, 29, 12, 12] 29 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 23] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29]) total number of confs: 97 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074231 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 8, 11, 5, 7, 7, 7, 6, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 3, 3, 3, 12, 12, 12, 12, 12, 1, 1, 1, 6, 6, 15, 15, 1, 2, 2, 2, 3, 12, 1, 1, 15, 15, 1, 1] 29 rigid atoms, others: [0, 1, 2, 11, 12, 13, 18, 24, 25, 28, 29] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 19, 20, 21, 22, 23, 26, 27]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074231 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074231 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074231/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074231 Building REAL250005074232 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074232' /scratch/stefan/7916156/working/building/REAL250005074232 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074232 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074232/0 /scratch/stefan/7916156/working/building/REAL250005074232 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 347) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/347 `/scratch/stefan/7916156/working/3D/347' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC1CC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074232.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074232/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074232 none CC1CC1CC(=O)N1CC(C)(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 104 conformations in input total number of sets (complete confs): 104 using faster count positions algorithm for large data unique positions, atoms: [70, 70, 70, 43, 6, 1, 6, 1, 1, 1, 1, 1, 3, 3, 3, 11, 11, 11, 11, 11, 1, 70, 70, 70, 70, 70, 70, 70, 43, 43, 1, 1, 2, 2, 2, 3, 11, 1, 1] 104 rigid atoms, others: [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, 32, 33, 34, 35, 36]) total number of confs: 258 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074232 none CC1CC1CC(=O)N1CC(C)(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 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, 8, 33, 33, 70, 70, 70, 70, 89, 89, 89, 104, 104, 104, 104, 104, 70, 2, 2, 2, 1, 1, 1, 1, 8, 8, 70, 70, 70, 70, 70, 89, 104, 70, 70] 104 rigid atoms, others: [0, 1, 2, 3, 4, 24, 25, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 254 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074232 none CC1CC1CC(=O)N1CC(C)(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 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, 92, 22, 11, 22, 11, 11, 8, 11, 8, 1, 8, 1, 1, 1, 1, 1, 1, 11, 104, 104, 104, 104, 104, 104, 104, 92, 92, 11, 11, 11, 11, 11, 8, 1, 11, 11] 104 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: 365 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074232 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074232 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074232/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074232 Building REAL250005074233 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074233' /scratch/stefan/7916156/working/building/REAL250005074233 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074233 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074233/0 /scratch/stefan/7916156/working/building/REAL250005074233 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 348) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/348 `/scratch/stefan/7916156/working/3D/348' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1(C(=O)N2CC(C)(NC(=O)C3=CC(=O)[N-]O3)C2)CC1) `REAL250005074233.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074233/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074233 none CCC1(C(=O)N2CC(C)(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 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [22, 17, 7, 1, 7, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 1, 17, 17, 22, 22, 22, 22, 22, 1, 1, 2, 2, 2, 3, 8, 1, 1, 17, 17, 17, 17] 31 rigid atoms, others: [33, 34, 3, 5, 6, 7, 8, 9, 18, 26, 27] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 35, 36, 37, 38]) total number of confs: 95 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074233 none CCC1(C(=O)N2CC(C)(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 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 1, 5, 5, 17, 17, 17, 17, 22, 22, 22, 29, 29, 29, 29, 29, 17, 1, 1, 4, 4, 4, 4, 4, 17, 17, 17, 17, 17, 22, 29, 17, 17, 1, 1, 1, 1] 31 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: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.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: REAL250005074233 none CCC1(C(=O)N2CC(C)(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 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [31, 29, 15, 8, 15, 8, 8, 6, 8, 6, 1, 6, 1, 1, 1, 1, 1, 1, 8, 29, 29, 31, 31, 31, 31, 31, 8, 8, 8, 8, 8, 6, 1, 8, 8, 29, 29, 29, 29] 31 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: 101 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074233 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074233 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074233/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074233 Building REAL250005074234 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074234' /scratch/stefan/7916156/working/building/REAL250005074234 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074234 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074234/0 /scratch/stefan/7916156/working/building/REAL250005074234 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 349) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/349 `/scratch/stefan/7916156/working/3D/349' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074234.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074234/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074234 none CC(C)(C)C(=O)N1CC(C)(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 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, 6, 10, 6, 6, 4, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 6, 6, 6, 6, 5, 1, 6, 6] 10 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: 36 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074234 none CC(C)(C)C(=O)N1CC(C)(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 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 6, 6, 1, 5, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 6, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 2, 2, 2, 2, 6, 1, 1] 10 rigid atoms, others: [4, 37, 6, 7, 8, 9, 10, 19, 36, 29, 30] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35]) total number of confs: 35 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074234 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074234 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074234/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074234 Building REAL250005074235 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074235' /scratch/stefan/7916156/working/building/REAL250005074235 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074235 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074235/0 /scratch/stefan/7916156/working/building/REAL250005074235 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 350) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/350 `/scratch/stefan/7916156/working/3D/350' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)CCC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074235.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074235/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074235 none C=C(C)CCC(=O)N1CC(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, 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 92 conformations in input total number of sets (complete confs): 92 using faster count positions algorithm for large data unique positions, atoms: [92, 89, 92, 80, 25, 12, 25, 12, 12, 8, 12, 8, 1, 8, 1, 1, 1, 1, 1, 1, 12, 92, 92, 92, 92, 92, 89, 89, 80, 80, 12, 12, 12, 12, 12, 8, 1, 12, 12] 92 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: 346 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074235 none C=C(C)CCC(=O)N1CC(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, 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 92 conformations in input total number of sets (complete confs): 92 using faster count positions algorithm for large data unique positions, atoms: [79, 60, 79, 42, 6, 1, 6, 1, 1, 1, 1, 1, 3, 3, 3, 12, 12, 12, 12, 12, 1, 79, 79, 79, 79, 79, 60, 60, 42, 42, 1, 1, 2, 2, 2, 3, 12, 1, 1] 92 rigid atoms, others: [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, 32, 33, 34, 35, 36]) total number of confs: 328 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074235 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074235 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074235/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074235 Building REAL250005074236 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074236' /scratch/stefan/7916156/working/building/REAL250005074236 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074236 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074236/0 /scratch/stefan/7916156/working/building/REAL250005074236 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 351) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/351 `/scratch/stefan/7916156/working/3D/351' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2(CF)CC2)C1) `REAL250005074236.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074236.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074236/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074236 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2(CF)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 15, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 10, 10, 10, 27, 27, 43, 50, 43, 43, 10, 10, 10, 10, 5, 1, 10, 10, 50, 50, 43, 43, 43, 43, 10, 10] 50 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 25] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 173 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074236 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2(CF)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 15, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 10, 1, 1, 1, 6, 6, 15, 39, 14, 14, 1, 2, 2, 2, 3, 10, 1, 1, 39, 39, 14, 15, 14, 14, 1, 1] 50 rigid atoms, others: [0, 1, 2, 34, 11, 12, 13, 35, 20, 26, 27] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074236 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2(CF)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 15, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 15, 26, 26, 26, 43, 43, 43, 43, 43, 14, 4, 1, 4, 1, 1, 10, 1, 1, 14, 15, 15, 15, 26, 43, 15, 15, 10, 10, 1, 1, 1, 1, 14, 14] 50 rigid atoms, others: [32, 33, 13, 15, 16, 18, 19, 30, 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, 34, 35]) total number of confs: 136 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074236 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074236 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074236/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074236 Building REAL250005074237 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074237' /scratch/stefan/7916156/working/building/REAL250005074237 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074237 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074237/0 /scratch/stefan/7916156/working/building/REAL250005074237 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 352) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/352 `/scratch/stefan/7916156/working/3D/352' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(C)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074237.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074237/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074237 none CC(C)C(C)C(=O)N1CC(C)(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 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 16, 29, 7, 16, 7, 7, 5, 7, 5, 1, 5, 1, 1, 1, 1, 1, 1, 7, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 7, 7, 7, 7, 7, 6, 1, 7, 7] 29 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: 102 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074237 none CC(C)C(C)C(=O)N1CC(C)(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 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [24, 21, 24, 7, 21, 1, 7, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 1, 24, 24, 24, 24, 24, 24, 24, 21, 21, 21, 21, 1, 1, 2, 2, 2, 3, 7, 1, 1] 29 rigid atoms, others: [32, 33, 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, 34, 35, 36, 37, 38]) total number of confs: 107 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074237 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074237 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074237/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074237 Building REAL250005074238 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074238' /scratch/stefan/7916156/working/building/REAL250005074238 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074238 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074238/0 /scratch/stefan/7916156/working/building/REAL250005074238 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 353) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/353 `/scratch/stefan/7916156/working/3D/353' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1C[C@H]1C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074238.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074238/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074238 none CC[C@@H]1C[C@H]1C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 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', '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, 7, 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, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [46, 29, 29, 29, 29, 7, 29, 1, 7, 1, 1, 1, 1, 1, 3, 3, 3, 13, 13, 13, 13, 13, 1, 46, 46, 46, 46, 46, 29, 29, 1, 1, 2, 2, 2, 3, 13, 1, 1] 73 rigid atoms, others: [37, 38, 7, 9, 10, 11, 12, 13, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 197 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074238 none CC[C@@H]1C[C@H]1C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 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', '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, 7, 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, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 9, 9, 29, 29, 29, 29, 41, 41, 41, 62, 62, 62, 62, 62, 29, 3, 3, 3, 3, 3, 1, 1, 29, 29, 29, 29, 29, 41, 62, 29, 29] 73 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 28, 29] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.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: REAL250005074238 none CC[C@@H]1C[C@H]1C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 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', '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, 7, 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, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 62, 62, 62, 62, 25, 62, 13, 25, 13, 13, 10, 13, 10, 1, 10, 1, 1, 1, 1, 1, 1, 13, 73, 73, 73, 73, 73, 62, 62, 13, 13, 13, 13, 13, 10, 1, 13, 13] 73 rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 235 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074238 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074238 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074238/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074238 Building REAL250005074239 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074239' /scratch/stefan/7916156/working/building/REAL250005074239 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074239 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074239/0 /scratch/stefan/7916156/working/building/REAL250005074239 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 354) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/354 `/scratch/stefan/7916156/working/3D/354' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2CC23CC3)C1) `REAL250005074239.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074239/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074239 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2CC23CC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 12, 12, 12, 26, 26, 48, 48, 48, 48, 12, 12, 12, 12, 7, 1, 12, 12, 48, 48, 48, 48, 48, 48, 48, 12, 12] 48 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 25] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 153 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074239 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2CC23CC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 3, 3, 3, 12, 12, 12, 12, 12, 1, 1, 1, 6, 6, 25, 25, 25, 25, 1, 2, 2, 2, 3, 12, 1, 1, 25, 25, 25, 25, 25, 25, 25, 1, 1] 48 rigid atoms, others: [0, 1, 2, 35, 36, 11, 12, 13, 20, 26, 27] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074239 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2CC23CC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 39, 39, 39, 48, 48, 48, 48, 48, 25, 7, 1, 7, 1, 1, 1, 1, 1, 25, 25, 25, 25, 39, 48, 25, 25, 1, 1, 1, 1, 1, 1, 1, 25, 25] 48 rigid atoms, others: [32, 33, 34, 13, 15, 16, 17, 18, 19, 28, 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, 35, 36]) total number of confs: 113 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074239 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074239 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074239/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074239 Building REAL250005074240 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074240' /scratch/stefan/7916156/working/building/REAL250005074240 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074240 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074240/0 /scratch/stefan/7916156/working/building/REAL250005074240 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 355) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/355 `/scratch/stefan/7916156/working/3D/355' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)[C@H]2CCCO2)C1) `REAL250005074240.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074240/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074240 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)[C@H]2CCCO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [11, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 11, 11, 11, 22, 22, 45, 45, 45, 45, 45, 11, 11, 11, 11, 6, 1, 11, 11, 45, 45, 45, 45, 45, 45, 11, 11] 45 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 26] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 131 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074240 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)[C@H]2CCCO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 3, 3, 3, 11, 11, 11, 11, 11, 1, 1, 1, 6, 6, 26, 26, 26, 26, 26, 1, 2, 2, 2, 3, 11, 1, 1, 26, 26, 26, 26, 26, 26, 1, 1] 45 rigid atoms, others: [0, 1, 2, 35, 36, 11, 12, 13, 21, 27, 28] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34]) 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.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: REAL250005074240 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)[C@H]2CCCO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 40, 40, 40, 45, 45, 45, 45, 45, 26, 10, 1, 10, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 40, 45, 26, 26, 1, 1, 1, 1, 1, 1, 26, 26] 45 rigid atoms, others: [32, 33, 34, 13, 15, 16, 17, 18, 19, 20, 29, 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, 35, 36]) total number of confs: 111 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074240 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074240 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074240/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074240 Building REAL250005074241 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074241' /scratch/stefan/7916156/working/building/REAL250005074241 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074241 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074241/0 /scratch/stefan/7916156/working/building/REAL250005074241 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 356) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/356 `/scratch/stefan/7916156/working/3D/356' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(CC(=O)N2CC(C)(NC(=O)C3=CC(=O)[N-]O3)C2)CC1) `REAL250005074241.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074241.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074241/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074241 none CC1(CC(=O)N2CC(C)(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 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [53, 29, 6, 1, 6, 1, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 8, 1, 53, 53, 53, 53, 53, 29, 29, 1, 1, 2, 2, 2, 2, 9, 1, 1, 53, 53, 53, 53] 76 rigid atoms, others: [33, 34, 3, 5, 6, 7, 8, 9, 18, 26, 27] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 35, 36, 37, 38]) total number of confs: 209 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074241 none CC1(CC(=O)N2CC(C)(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 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 9, 27, 27, 53, 53, 53, 53, 67, 67, 67, 76, 76, 76, 76, 76, 53, 1, 1, 2, 2, 2, 9, 9, 53, 53, 53, 53, 53, 67, 76, 53, 53, 1, 1, 1, 1] 76 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: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074241 none CC1(CC(=O)N2CC(C)(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 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [76, 55, 20, 9, 20, 9, 9, 7, 8, 7, 1, 7, 1, 1, 1, 1, 1, 1, 8, 76, 76, 76, 76, 76, 55, 55, 9, 9, 9, 9, 9, 7, 1, 9, 8, 76, 76, 76, 76] 76 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: 290 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074241 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074241 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074241/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074241 Building REAL250005074242 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074242' /scratch/stefan/7916156/working/building/REAL250005074242 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074242 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074242/0 /scratch/stefan/7916156/working/building/REAL250005074242 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 357) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/357 `/scratch/stefan/7916156/working/3D/357' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C(=O)N2CC(C)(NC(=O)C3=CC(=O)[N-]O3)C2)CC1) `REAL250005074242.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074242/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074242 none CC1(C(=O)N2CC(C)(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 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 1, 4, 1, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 5, 1, 9, 9, 9, 9, 9, 1, 1, 2, 2, 2, 3, 5, 1, 1, 9, 9, 9, 9] 14 rigid atoms, others: [2, 4, 5, 6, 7, 8, 17, 23, 24, 30, 31] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 32, 33, 34, 35]) total number of confs: 38 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074242 none CC1(C(=O)N2CC(C)(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 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 5, 5, 9, 9, 9, 9, 12, 12, 12, 14, 14, 14, 14, 14, 9, 1, 1, 2, 2, 2, 9, 9, 9, 9, 9, 12, 14, 9, 9, 1, 1, 1, 1] 14 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: 40 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.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: REAL250005074242 none CC1(C(=O)N2CC(C)(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 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [14, 9, 5, 9, 5, 5, 3, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 14, 14, 14, 14, 14, 5, 5, 5, 5, 5, 3, 1, 5, 5, 14, 14, 14, 14] 14 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: 41 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074242 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074242 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074242/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074242 Building REAL250005074243 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074243' /scratch/stefan/7916156/working/building/REAL250005074243 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074243 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074243/0 /scratch/stefan/7916156/working/building/REAL250005074243 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 358) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/358 `/scratch/stefan/7916156/working/3D/358' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=CNC=C2)C1) `REAL250005074243.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074243/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074243 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=CNC=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 1, 8, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [13, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 13, 13, 13, 26, 26, 73, 73, 73, 73, 13, 13, 13, 13, 7, 1, 13, 13, 73, 73, 73, 73, 13, 13] 73 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 25] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 150 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074243 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=CNC=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 1, 8, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 3, 3, 3, 13, 13, 13, 13, 13, 1, 1, 1, 6, 6, 45, 45, 45, 45, 1, 2, 2, 2, 3, 13, 1, 1, 45, 45, 45, 45, 1, 1] 73 rigid atoms, others: [0, 1, 2, 33, 32, 11, 12, 13, 20, 26, 27] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30, 31]) total number of confs: 82 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.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: REAL250005074243 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=CNC=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 1, 8, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 45, 63, 63, 63, 73, 73, 73, 73, 73, 45, 10, 1, 10, 1, 1, 1, 1, 1, 45, 45, 45, 45, 63, 73, 45, 45, 1, 1, 1, 1, 45, 45] 73 rigid atoms, others: [13, 15, 16, 17, 18, 19, 28, 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, 32, 33]) total number of confs: 158 number of broken/clashed sets: 5 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074243 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074243 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074243/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074243 Building REAL250005074244 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074244' /scratch/stefan/7916156/working/building/REAL250005074244 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074244 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074244/0 /scratch/stefan/7916156/working/building/REAL250005074244 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 359) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/359 `/scratch/stefan/7916156/working/3D/359' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=CN=CO2)C1) `REAL250005074244.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074244/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074244 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=CN=CO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 1, 8, 1, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 7, 7, 7, 18, 18, 27, 27, 27, 27, 7, 7, 7, 7, 5, 1, 7, 7, 27, 27, 7, 7] 27 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 25] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31]) total number of confs: 63 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074244 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=CN=CO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 1, 8, 1, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 1, 1, 1, 6, 6, 14, 14, 14, 14, 1, 2, 2, 2, 3, 7, 1, 1, 14, 14, 1, 1] 27 rigid atoms, others: [0, 1, 2, 11, 12, 13, 20, 26, 27, 30, 31] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074244 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=CN=CO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 1, 8, 1, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 25, 25, 25, 27, 27, 27, 27, 27, 14, 9, 1, 9, 1, 1, 1, 1, 1, 14, 14, 14, 14, 25, 27, 14, 14, 1, 1, 14, 14] 27 rigid atoms, others: [13, 15, 16, 17, 18, 19, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31]) total number of confs: 75 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074244 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074244 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074244/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074244 Building REAL250005074245 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074245' /scratch/stefan/7916156/working/building/REAL250005074245 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074245 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074245/0 /scratch/stefan/7916156/working/building/REAL250005074245 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 360) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/360 `/scratch/stefan/7916156/working/3D/360' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(C)(C)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074245.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074245/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074245 none C=CC(C)(C)C(=O)N1CC(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, 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 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 21, 25, 25, 8, 21, 8, 8, 6, 8, 6, 1, 6, 1, 1, 1, 1, 1, 1, 8, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8, 8, 8, 8, 8, 6, 1, 8, 8] 25 rigid atoms, others: [36, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 77 number of broken/clashed sets: 11 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074245 none C=CC(C)(C)C(=O)N1CC(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, 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 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [19, 13, 7, 13, 13, 1, 7, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 1, 19, 19, 19, 13, 13, 13, 13, 13, 13, 1, 1, 2, 2, 2, 3, 8, 1, 1] 25 rigid atoms, others: [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, 32, 33, 34, 35, 36]) total number of confs: 85 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074245 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074245 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074245/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074245 Building REAL250005074246 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074246' /scratch/stefan/7916156/working/building/REAL250005074246 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074246 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074246/0 /scratch/stefan/7916156/working/building/REAL250005074246 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 361) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/361 `/scratch/stefan/7916156/working/3D/361' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H]1C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074246.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074246/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074246 none C[C@@H]1C[C@H]1C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 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, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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: [20, 20, 20, 20, 6, 20, 1, 6, 1, 1, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 9, 1, 20, 20, 20, 20, 20, 1, 1, 2, 2, 2, 2, 9, 1, 1] 31 rigid atoms, others: [34, 35, 6, 8, 9, 10, 11, 12, 21, 27, 28] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 70 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074246 none C[C@@H]1C[C@H]1C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 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, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 8, 8, 20, 20, 20, 20, 27, 27, 27, 31, 31, 31, 31, 31, 20, 2, 2, 2, 1, 1, 20, 20, 20, 20, 20, 27, 31, 20, 20] 31 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 25, 26] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35]) 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.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: REAL250005074246 none C[C@@H]1C[C@H]1C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 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, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 20, 31, 9, 20, 9, 9, 6, 9, 6, 1, 6, 1, 1, 1, 1, 1, 1, 9, 31, 31, 31, 31, 31, 9, 9, 10, 10, 10, 6, 1, 9, 9] 31 rigid atoms, others: [33, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35]) total number of confs: 103 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074246 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074246 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074246/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074246 Building REAL250005074247 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074247' /scratch/stefan/7916156/working/building/REAL250005074247 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074247 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074247/0 /scratch/stefan/7916156/working/building/REAL250005074247 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 362) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/362 `/scratch/stefan/7916156/working/3D/362' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2(C)CCC2)C1) `REAL250005074247.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074247/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074247 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2(C)CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [11, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 11, 11, 11, 17, 17, 19, 19, 19, 19, 11, 11, 11, 11, 8, 1, 11, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 11, 11] 19 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 25] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 55 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074247 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2(C)CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 3, 3, 3, 11, 11, 11, 11, 11, 1, 1, 1, 6, 6, 9, 9, 9, 9, 1, 2, 2, 2, 3, 11, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1] 19 rigid atoms, others: [0, 1, 2, 37, 38, 11, 12, 13, 20, 26, 27] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074247 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2(C)CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 15, 15, 15, 19, 19, 19, 19, 19, 9, 3, 1, 3, 1, 1, 1, 1, 1, 9, 9, 9, 9, 15, 19, 9, 9, 2, 2, 2, 1, 1, 1, 1, 1, 1, 9, 9] 19 rigid atoms, others: [32, 33, 34, 35, 36, 13, 15, 16, 17, 18, 19, 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, 30, 37, 38]) total number of confs: 52 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074247 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074247 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074247/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074247 Building REAL250005074248 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074248' /scratch/stefan/7916156/working/building/REAL250005074248 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074248 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074248/0 /scratch/stefan/7916156/working/building/REAL250005074248 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 363) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/363 `/scratch/stefan/7916156/working/3D/363' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(F)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074248.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074248/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074248 none CCC(F)C(=O)N1CC(C)(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 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [45, 44, 19, 44, 8, 19, 8, 8, 6, 8, 6, 1, 6, 1, 1, 1, 1, 1, 1, 8, 45, 45, 45, 45, 45, 44, 8, 8, 8, 8, 8, 7, 1, 8, 8] 45 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: 166 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074248 none CCC(F)C(=O)N1CC(C)(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 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [34, 24, 5, 24, 1, 5, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 1, 34, 34, 34, 34, 34, 24, 1, 1, 2, 2, 2, 3, 8, 1, 1] 45 rigid atoms, others: [33, 34, 4, 6, 7, 8, 9, 10, 19, 26, 27] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074248 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074248 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074248/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074248 Building REAL250005074249 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074249' /scratch/stefan/7916156/working/building/REAL250005074249 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074249 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074249/0 /scratch/stefan/7916156/working/building/REAL250005074249 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 364) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/364 `/scratch/stefan/7916156/working/3D/364' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)CCCF)C1) `REAL250005074249.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074249/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074249 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)CCCF)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 15, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 193 conformations in input total number of sets (complete confs): 193 using faster count positions algorithm for large data unique positions, atoms: [16, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 16, 16, 16, 45, 45, 148, 187, 193, 16, 16, 16, 16, 9, 1, 16, 16, 148, 148, 193, 193, 193, 193, 16, 16] 193 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 24] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 843 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074249 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)CCCF)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 15, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 193 conformations in input total number of sets (complete confs): 193 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 3, 3, 3, 16, 16, 16, 16, 16, 1, 1, 1, 6, 6, 43, 66, 121, 1, 2, 2, 2, 3, 16, 1, 1, 43, 43, 72, 72, 119, 118, 1, 1] 193 rigid atoms, others: [0, 1, 2, 34, 33, 11, 12, 13, 19, 25, 26] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32]) total number of confs: 582 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074249 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074249 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074249/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074249 Building REAL250005074250 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074250' /scratch/stefan/7916156/working/building/REAL250005074250 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074250 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074250/0 /scratch/stefan/7916156/working/building/REAL250005074250 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 365) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/365 `/scratch/stefan/7916156/working/3D/365' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@@H]1C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074250.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074250.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074250/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074250 none C[C@H]1C[C@@H]1C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 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, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 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: [18, 18, 18, 18, 6, 18, 1, 6, 1, 1, 1, 1, 1, 2, 2, 2, 10, 10, 10, 10, 10, 1, 18, 18, 18, 18, 18, 1, 1, 2, 2, 2, 2, 10, 1, 1] 28 rigid atoms, others: [34, 35, 6, 8, 9, 10, 11, 12, 21, 27, 28] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 65 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074250 none C[C@H]1C[C@@H]1C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 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, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 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: [1, 1, 1, 1, 1, 1, 1, 8, 8, 18, 18, 18, 18, 24, 24, 24, 28, 28, 28, 28, 28, 18, 2, 2, 2, 1, 1, 18, 18, 18, 18, 18, 24, 28, 18, 18] 28 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 25, 26] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074250 none C[C@H]1C[C@@H]1C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 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, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 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, 28, 28, 28, 21, 28, 10, 21, 10, 10, 8, 10, 8, 1, 8, 1, 1, 1, 1, 1, 1, 10, 28, 28, 28, 28, 28, 10, 10, 10, 10, 10, 8, 1, 10, 10] 28 rigid atoms, others: [33, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35]) total number of confs: 83 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074250 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074250 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074250/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074250 Building REAL250005074251 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074251' /scratch/stefan/7916156/working/building/REAL250005074251 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074251 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074251/0 /scratch/stefan/7916156/working/building/REAL250005074251 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 366) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/366 `/scratch/stefan/7916156/working/3D/366' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(F)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074251.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074251/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074251 none CC(C)C(F)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 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', '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, 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, 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] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [53, 50, 52, 21, 50, 9, 21, 9, 9, 6, 9, 6, 1, 6, 1, 1, 1, 1, 1, 1, 9, 53, 53, 53, 53, 53, 53, 53, 50, 9, 9, 9, 9, 9, 6, 1, 9, 9] 53 rigid atoms, others: [35, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37]) total number of confs: 202 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074251 none CC(C)C(F)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 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', '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, 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, 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] 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: [41, 36, 40, 6, 36, 1, 6, 1, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 1, 41, 41, 41, 41, 41, 41, 41, 36, 1, 1, 2, 2, 2, 3, 9, 1, 1] 53 rigid atoms, others: [36, 5, 7, 8, 9, 10, 11, 20, 29, 30, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35]) total number of confs: 175 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074251 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074251 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074251/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074251 Building REAL250005074252 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074252' /scratch/stefan/7916156/working/building/REAL250005074252 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074252 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074252/0 /scratch/stefan/7916156/working/building/REAL250005074252 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 367) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/367 `/scratch/stefan/7916156/working/3D/367' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=NNN=C2)C1) `REAL250005074252.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074252/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074252 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=NNN=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 8, 8, 8, 1, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 7, 7, 7, 20, 20, 30, 30, 30, 30, 7, 7, 7, 7, 5, 1, 7, 7, 30, 30, 7, 7] 30 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 25] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31]) total number of confs: 73 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074252 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=NNN=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 8, 8, 8, 1, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 7, 7, 7, 7, 7, 1, 1, 1, 6, 6, 16, 16, 16, 16, 1, 2, 2, 2, 3, 7, 1, 1, 16, 16, 1, 1] 30 rigid atoms, others: [0, 1, 2, 11, 12, 13, 20, 26, 27, 30, 31] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29]) 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.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: REAL250005074252 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=NNN=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 8, 8, 8, 1, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 27, 27, 27, 30, 30, 30, 30, 30, 16, 11, 1, 11, 1, 1, 1, 1, 1, 16, 16, 16, 16, 27, 30, 16, 16, 1, 1, 16, 16] 30 rigid atoms, others: [13, 15, 16, 17, 18, 19, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31]) total number of confs: 81 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074252 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074252 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074252/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074252 Building REAL250005074253 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074253' /scratch/stefan/7916156/working/building/REAL250005074253 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074253 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074253/0 /scratch/stefan/7916156/working/building/REAL250005074253 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 368) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/368 `/scratch/stefan/7916156/working/3D/368' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)CO)C1) `REAL250005074253.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074253/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074253 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)CO)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [13, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 13, 13, 13, 18, 18, 22, 13, 13, 13, 13, 8, 1, 13, 13, 22, 22, 66, 13, 13] 66 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 22] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 147 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074253 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)CO)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 3, 3, 3, 13, 13, 13, 13, 13, 1, 1, 1, 3, 3, 11, 1, 2, 2, 2, 3, 13, 1, 1, 11, 11, 33, 1, 1] 66 rigid atoms, others: [0, 1, 2, 11, 12, 13, 17, 23, 24, 28, 29] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 18, 19, 20, 21, 22, 25, 26, 27]) total number of confs: 94 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074253 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074253 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074253/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074253 Building REAL250005074254 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074254' /scratch/stefan/7916156/working/building/REAL250005074254 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074254 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074254/0 /scratch/stefan/7916156/working/building/REAL250005074254 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 369) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/369 `/scratch/stefan/7916156/working/3D/369' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C=CC(N)=O)C1) `REAL250005074254.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074254/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074254 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C=CC(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 1, 1, 8, 11, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [13, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 13, 13, 13, 21, 21, 43, 43, 52, 52, 13, 13, 13, 13, 8, 1, 13, 13, 43, 43, 52, 52, 13, 13] 52 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 25] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 157 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074254 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C=CC(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 1, 1, 8, 11, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 3, 3, 3, 13, 13, 13, 13, 13, 1, 1, 1, 6, 6, 27, 27, 39, 39, 1, 2, 2, 2, 3, 13, 1, 1, 27, 27, 39, 39, 1, 1] 52 rigid atoms, others: [0, 1, 2, 33, 32, 11, 12, 13, 20, 26, 27] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30, 31]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074254 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074254 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074254/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074254 Building REAL250005074255 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074255' /scratch/stefan/7916156/working/building/REAL250005074255 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074255 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074255/0 /scratch/stefan/7916156/working/building/REAL250005074255 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 370) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/370 `/scratch/stefan/7916156/working/3D/370' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074255.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074255/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074255 none COC(=O)CC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 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', 'C.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, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 69, 100, 20, 9, 20, 9, 9, 7, 9, 7, 1, 7, 1, 1, 1, 1, 1, 1, 9, 100, 100, 100, 69, 69, 9, 9, 9, 9, 9, 7, 1, 9, 9] 100 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: 353 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074255 none COC(=O)CC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 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', 'C.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, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [89, 89, 36, 89, 6, 1, 6, 1, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 1, 89, 89, 89, 36, 36, 1, 1, 2, 2, 2, 3, 9, 1, 1] 100 rigid atoms, others: [33, 34, 5, 7, 8, 9, 10, 11, 20, 26, 27] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32]) total number of confs: 292 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074255 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074255 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074255/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074255 Building REAL250005074256 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074256' /scratch/stefan/7916156/working/building/REAL250005074256 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074256 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074256/0 /scratch/stefan/7916156/working/building/REAL250005074256 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 371) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/371 `/scratch/stefan/7916156/working/3D/371' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSC=CC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074256.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074256.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074256/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074256 none CSC=CC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 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', 'C.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, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 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, 36, 36, 17, 9, 17, 9, 9, 7, 9, 7, 1, 7, 1, 1, 1, 1, 1, 1, 9, 47, 47, 47, 36, 36, 9, 9, 9, 9, 9, 8, 1, 9, 9] 47 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33]) total number of confs: 123 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074256 none CSC=CC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 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', 'C.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, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 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: [38, 21, 21, 6, 1, 6, 1, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 1, 39, 39, 39, 21, 21, 1, 1, 2, 2, 2, 3, 9, 1, 1] 47 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 19, 25, 26] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074256 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074256 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074256/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074256 Building REAL250005074257 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074257' /scratch/stefan/7916156/working/building/REAL250005074257 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074257 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074257/0 /scratch/stefan/7916156/working/building/REAL250005074257 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 372) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/372 `/scratch/stefan/7916156/working/3D/372' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)CCC(N)=O)C1) `REAL250005074257.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074257/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074257 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)CCC(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.am', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 1, 8, 11, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [7, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 19, 19, 52, 70, 86, 86, 7, 7, 7, 7, 3, 1, 7, 7, 52, 52, 70, 70, 86, 86, 7, 7] 86 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 25] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 367 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074257 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)CCC(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.am', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 1, 8, 11, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 1, 1, 1, 5, 5, 23, 41, 71, 71, 1, 2, 2, 2, 3, 7, 1, 1, 23, 23, 41, 41, 71, 71, 1, 1] 86 rigid atoms, others: [0, 1, 2, 34, 11, 12, 13, 35, 20, 26, 27] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33]) total number of confs: 289 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074257 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074257 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074257/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074257 Building REAL250005074258 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074258' /scratch/stefan/7916156/working/building/REAL250005074258 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074258 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074258/0 /scratch/stefan/7916156/working/building/REAL250005074258 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 373) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/373 `/scratch/stefan/7916156/working/3D/373' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2CCO2)C1) `REAL250005074258.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074258/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074258 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2CCO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [13, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 13, 13, 13, 24, 24, 32, 32, 32, 13, 13, 13, 13, 6, 1, 13, 13, 32, 32, 32, 32, 32, 13, 13] 32 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 24] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 99 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074258 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2CCO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 3, 3, 3, 13, 13, 13, 13, 13, 1, 1, 1, 5, 5, 19, 19, 19, 1, 2, 2, 2, 3, 13, 1, 1, 19, 19, 19, 19, 19, 1, 1] 32 rigid atoms, others: [0, 1, 2, 33, 32, 11, 12, 13, 19, 25, 26] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074258 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2CCO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [19, 19, 19, 29, 29, 29, 32, 32, 32, 32, 32, 19, 9, 1, 9, 1, 1, 1, 1, 19, 19, 19, 19, 29, 32, 19, 19, 1, 1, 1, 1, 1, 19, 19] 32 rigid atoms, others: [13, 15, 16, 17, 18, 27, 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, 32, 33]) total number of confs: 81 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074258 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074258 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074258/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074258 Building REAL250005074259 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074259' /scratch/stefan/7916156/working/building/REAL250005074259 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074259 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074259/0 /scratch/stefan/7916156/working/building/REAL250005074259 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 374) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/374 `/scratch/stefan/7916156/working/3D/374' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2(Cl)CC2)C1) `REAL250005074259.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074259/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074259 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2(Cl)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'Cl', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 16, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 11, 11, 11, 20, 20, 26, 26, 26, 11, 11, 11, 11, 6, 1, 11, 11, 26, 26, 26, 26, 11, 11] 26 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 24] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 83 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074259 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2(Cl)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'Cl', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 16, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 3, 3, 3, 11, 11, 11, 11, 11, 1, 1, 1, 6, 6, 15, 15, 15, 1, 2, 2, 2, 3, 11, 1, 1, 15, 15, 15, 15, 1, 1] 26 rigid atoms, others: [0, 1, 2, 32, 11, 12, 13, 19, 25, 26, 31] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 27, 28, 29, 30]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up 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: REAL250005074259 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2(Cl)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'Cl', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 16, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 21, 21, 21, 26, 26, 26, 26, 26, 15, 7, 1, 7, 1, 1, 1, 1, 15, 15, 15, 15, 21, 26, 15, 15, 1, 1, 1, 1, 15, 15] 26 rigid atoms, others: [13, 15, 16, 17, 18, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32]) total number of confs: 61 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074259 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074259 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074259/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074259 Building REAL250005074260 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074260' /scratch/stefan/7916156/working/building/REAL250005074260 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074260 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074260/0 /scratch/stefan/7916156/working/building/REAL250005074260 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 375) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/375 `/scratch/stefan/7916156/working/3D/375' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=CCCO2)C1) `REAL250005074260.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074260/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074260 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=CCCO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 1, 5, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [12, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 12, 12, 12, 25, 25, 37, 37, 37, 37, 12, 12, 12, 12, 8, 1, 12, 12, 37, 37, 37, 37, 37, 12, 12] 37 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 25] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 91 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074260 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=CCCO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 1, 5, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 3, 3, 3, 12, 12, 12, 12, 12, 1, 1, 1, 6, 6, 17, 17, 17, 17, 1, 2, 2, 2, 3, 12, 1, 1, 18, 17, 17, 17, 17, 1, 1] 37 rigid atoms, others: [0, 1, 2, 34, 33, 11, 12, 13, 20, 26, 27] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up 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: REAL250005074260 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=CCCO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 1, 5, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [18, 18, 18, 31, 31, 31, 37, 37, 37, 37, 37, 18, 9, 1, 9, 1, 1, 1, 1, 1, 17, 18, 18, 18, 31, 37, 18, 18, 1, 1, 1, 1, 1, 18, 17] 37 rigid atoms, others: [32, 13, 15, 16, 17, 18, 19, 28, 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, 33, 34]) total number of confs: 101 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074260 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074260 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074260/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074260 Building REAL250005074261 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074261' /scratch/stefan/7916156/working/building/REAL250005074261 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074261 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074261/0 /scratch/stefan/7916156/working/building/REAL250005074261 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 376) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/376 `/scratch/stefan/7916156/working/3D/376' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2COC2)C1) `REAL250005074261.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074261/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074261 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2COC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [14, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 14, 14, 14, 27, 27, 34, 34, 34, 14, 14, 14, 14, 7, 1, 14, 14, 34, 34, 34, 34, 34, 14, 14] 34 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 24] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 113 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074261 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2COC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 3, 3, 3, 14, 14, 14, 14, 14, 1, 1, 1, 4, 4, 17, 17, 17, 1, 2, 2, 2, 3, 14, 1, 1, 17, 17, 17, 17, 17, 1, 1] 34 rigid atoms, others: [0, 1, 2, 33, 32, 11, 12, 13, 19, 25, 26] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074261 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2COC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 29, 29, 29, 34, 34, 34, 34, 34, 17, 8, 1, 8, 1, 1, 1, 1, 17, 17, 17, 17, 29, 34, 17, 17, 1, 1, 1, 1, 1, 17, 17] 34 rigid atoms, others: [13, 15, 16, 17, 18, 27, 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, 32, 33]) total number of confs: 89 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074261 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074261 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074261/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074261 Building REAL250005074262 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074262' /scratch/stefan/7916156/working/building/REAL250005074262 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074262 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074262/0 /scratch/stefan/7916156/working/building/REAL250005074262 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 377) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/377 `/scratch/stefan/7916156/working/3D/377' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C=CCO)C1) `REAL250005074262.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074262/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074262 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C=CCO)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 1, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 183 conformations in input total number of sets (complete confs): 183 using faster count positions algorithm for large data unique positions, atoms: [13, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 13, 13, 13, 26, 26, 46, 46, 61, 13, 13, 13, 13, 7, 1, 13, 13, 46, 46, 61, 61, 183, 13, 13] 183 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 24] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 406 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074262 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C=CCO)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 1, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 183 conformations in input total number of sets (complete confs): 183 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 3, 3, 3, 13, 13, 13, 13, 13, 1, 1, 1, 6, 6, 24, 24, 53, 1, 2, 2, 2, 3, 13, 1, 1, 24, 24, 53, 53, 159, 1, 1] 183 rigid atoms, others: [0, 1, 2, 33, 32, 11, 12, 13, 19, 25, 26] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31]) total number of confs: 365 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074262 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074262 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074262/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074262 Building REAL250005074263 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074263' /scratch/stefan/7916156/working/building/REAL250005074263 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074263 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074263/0 /scratch/stefan/7916156/working/building/REAL250005074263 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 378) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/378 `/scratch/stefan/7916156/working/3D/378' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC(O)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074263.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074263.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074263/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074263 none CC=CC(O)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 12, 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, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 40, 15, 40, 8, 15, 8, 8, 6, 8, 6, 1, 6, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 40, 120, 8, 8, 8, 8, 8, 7, 1, 8, 8] 150 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: 312 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074263 none CC=CC(O)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 12, 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, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 24, 6, 24, 1, 6, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 1, 37, 37, 37, 37, 37, 24, 72, 1, 1, 2, 2, 2, 3, 8, 1, 1] 150 rigid atoms, others: [35, 36, 5, 7, 8, 9, 10, 11, 20, 28, 29] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34]) total number of confs: 223 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074263 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074263 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074263/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074263 Building REAL250005074264 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074264' /scratch/stefan/7916156/working/building/REAL250005074264 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005074264 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074264/0 /scratch/stefan/7916156/working/building/REAL250005074264 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 379) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/379 `/scratch/stefan/7916156/working/3D/379' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1)[NH+](C)C) `REAL250005074264.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074264.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074264/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074264 none C[C@@H](C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1)[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', '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, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 2, 3, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 1, 1, 2, 2, 3, 3, 3, 3, 3, 3] 3 rigid atoms, others: [32, 7, 9, 10, 11, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 9 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074264 none C[C@@H](C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1)[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', '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, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 1, 3, 3, 3, 3, 3, 3, 3, 1, 1, 2, 2, 2, 2, 2, 1, 1, 3, 3, 3, 3, 3, 3] 3 rigid atoms, others: [33, 34, 3, 5, 6, 7, 8, 9, 18, 26, 27] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40]) total number of confs: 17 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074264 /scratch/stefan/7916156/working /scratch/stefan/7916156 mkdir: created directory `1' /scratch/stefan/7916156/working/building/REAL250005074264/1 /scratch/stefan/7916156/working/building/REAL250005074264 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 1 (index: 380) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/380 `/scratch/stefan/7916156/working/3D/380' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1)N(C)C) `REAL250005074264.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005074264.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074264/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074264 none C[C@@H](C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', '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, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 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 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [14, 10, 14, 4, 10, 4, 4, 2, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 14, 15, 15, 14, 14, 14, 4, 4, 4, 4, 4, 3, 1, 4, 3, 15, 15, 15, 15, 15, 15] 15 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 62 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074264 none C[C@@H](C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', '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, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 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 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [12, 7, 12, 1, 7, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 3, 1, 12, 13, 13, 12, 12, 12, 1, 1, 2, 2, 2, 2, 4, 1, 1, 13, 13, 13, 13, 13, 13] 15 rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 18, 25, 26] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39]) total number of confs: 57 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074264 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074264 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 1: /scratch/stefan/7916156/working/building/REAL250005074264/1.* 0: /scratch/stefan/7916156/working/building/REAL250005074264/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074264 Building REAL250005074265 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074265' /scratch/stefan/7916156/working/building/REAL250005074265 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074265 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074265/0 /scratch/stefan/7916156/working/building/REAL250005074265 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 381) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/381 `/scratch/stefan/7916156/working/3D/381' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC=C(F)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074265.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074265/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074265 none CCC=C(F)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 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', 'C.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, 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 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [69, 48, 48, 18, 48, 8, 18, 8, 8, 6, 8, 6, 1, 6, 1, 1, 1, 1, 1, 1, 8, 69, 69, 69, 69, 69, 48, 8, 8, 8, 8, 8, 7, 1, 8, 8] 69 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: 267 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074265 none CCC=C(F)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 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', 'C.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, 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 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [52, 32, 32, 6, 32, 1, 6, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 1, 52, 52, 52, 52, 52, 32, 1, 1, 2, 2, 2, 3, 8, 1, 1] 69 rigid atoms, others: [34, 35, 5, 7, 8, 9, 10, 11, 20, 27, 28] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074265 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074265 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074265/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074265 Building REAL250005074266 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074266' /scratch/stefan/7916156/working/building/REAL250005074266 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074266 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074266/0 /scratch/stefan/7916156/working/building/REAL250005074266 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 382) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/382 `/scratch/stefan/7916156/working/3D/382' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC=CC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074266.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074266/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074266 none CCC=CC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 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 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [49, 35, 35, 20, 8, 20, 8, 8, 6, 8, 6, 1, 6, 1, 1, 1, 1, 1, 1, 8, 49, 49, 49, 49, 49, 35, 35, 8, 8, 8, 8, 8, 7, 1, 8, 8] 49 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: 187 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074266 none CCC=CC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 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 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [36, 24, 24, 6, 1, 6, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 1, 36, 36, 36, 36, 36, 24, 24, 1, 1, 2, 2, 2, 3, 8, 1, 1] 49 rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 10, 19, 27, 28] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074266 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074266 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074266/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074266 Building REAL250005074267 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074267' /scratch/stefan/7916156/working/building/REAL250005074267 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074267 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074267/0 /scratch/stefan/7916156/working/building/REAL250005074267 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 383) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/383 `/scratch/stefan/7916156/working/3D/383' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)CCN=[N+]=[N-])C1) `REAL250005074267.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074267.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074267/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074267 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)CCN=[N+]=[N-])C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.2', 'N.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 195 conformations in input total number of sets (complete confs): 195 using faster count positions algorithm for large data unique positions, atoms: [13, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 13, 13, 13, 38, 38, 124, 145, 195, 195, 13, 13, 13, 13, 6, 1, 13, 13, 124, 124, 145, 145, 13, 13] 195 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 25] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 646 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074267 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)CCN=[N+]=[N-])C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.2', 'N.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 195 conformations in input total number of sets (complete confs): 195 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 3, 3, 3, 13, 13, 13, 13, 13, 1, 1, 1, 6, 6, 40, 62, 144, 144, 1, 2, 2, 2, 3, 13, 1, 1, 40, 40, 62, 62, 1, 1] 195 rigid atoms, others: [0, 1, 2, 33, 32, 11, 12, 13, 20, 26, 27] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30, 31]) total number of confs: 397 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074267 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074267 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074267/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074267 Building REAL250005074268 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074268' /scratch/stefan/7916156/working/building/REAL250005074268 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074268 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074268/0 /scratch/stefan/7916156/working/building/REAL250005074268 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 384) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/384 `/scratch/stefan/7916156/working/3D/384' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCOCC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074268.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074268.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074268/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074268 none C#CCOCC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 5, 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, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 159, 94, 21, 8, 21, 8, 8, 6, 8, 6, 1, 6, 1, 1, 1, 1, 1, 1, 8, 201, 201, 201, 94, 94, 8, 8, 8, 8, 8, 6, 1, 8, 8] 201 rigid atoms, others: [32, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34]) total number of confs: 666 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074268 none C#CCOCC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 5, 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, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [180, 180, 111, 44, 6, 1, 6, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 1, 180, 180, 180, 44, 44, 1, 1, 2, 2, 2, 3, 8, 1, 1] 201 rigid atoms, others: [33, 34, 5, 7, 8, 9, 10, 11, 20, 26, 27] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32]) total number of confs: 600 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074268 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074268 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074268/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074268 Building REAL250005074269 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074269' /scratch/stefan/7916156/working/building/REAL250005074269 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074269 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074269/0 /scratch/stefan/7916156/working/building/REAL250005074269 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 385) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/385 `/scratch/stefan/7916156/working/3D/385' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)CCC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074269.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074269.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074269/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074269 none CC(O)CCC(=O)N1CC(C)(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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 237 conformations in input total number of sets (complete confs): 237 using faster count positions algorithm for large data unique positions, atoms: [79, 57, 79, 51, 15, 6, 15, 6, 6, 4, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 6, 79, 79, 79, 78, 237, 62, 62, 51, 51, 6, 6, 6, 6, 6, 4, 1, 6, 6] 237 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: 596 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074269 none CC(O)CCC(=O)N1CC(C)(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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 237 conformations in input total number of sets (complete confs): 237 using faster count positions algorithm for large data unique positions, atoms: [70, 39, 70, 32, 6, 1, 6, 1, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 6, 1, 70, 70, 70, 68, 210, 46, 46, 32, 32, 1, 1, 2, 2, 2, 3, 6, 1, 1] 237 rigid atoms, others: [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, 32, 33, 34, 35, 36]) total number of confs: 557 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074269 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074269 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074269/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074269 Building REAL250005074270 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074270' /scratch/stefan/7916156/working/building/REAL250005074270 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074270 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074270/0 /scratch/stefan/7916156/working/building/REAL250005074270 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 386) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/386 `/scratch/stefan/7916156/working/3D/386' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074270.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074270/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074270 none C#CCCC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 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, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 49, 18, 9, 18, 9, 9, 7, 9, 7, 1, 7, 1, 1, 1, 1, 1, 1, 9, 56, 56, 56, 49, 49, 9, 9, 9, 9, 9, 7, 1, 9, 9] 56 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33]) total number of confs: 212 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074270 none C#CCCC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 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, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [40, 40, 29, 5, 1, 5, 1, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 1, 40, 40, 40, 29, 29, 1, 1, 2, 2, 2, 3, 9, 1, 1] 56 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 19, 25, 26] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074270 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074270 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074270/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074270 Building REAL250005074271 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074271' /scratch/stefan/7916156/working/building/REAL250005074271 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074271 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074271/0 /scratch/stefan/7916156/working/building/REAL250005074271 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 387) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/387 `/scratch/stefan/7916156/working/3D/387' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC=CC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074271.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074271/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074271 none CC=CC=CC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 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 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 34, 34, 17, 7, 17, 7, 7, 5, 7, 5, 1, 5, 1, 1, 1, 1, 1, 1, 7, 37, 37, 37, 37, 37, 34, 34, 7, 7, 7, 7, 7, 6, 1, 7, 7] 37 rigid atoms, others: [34, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36]) total number of confs: 115 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074271 none CC=CC=CC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 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 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 20, 20, 5, 1, 5, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 1, 29, 29, 29, 28, 28, 20, 20, 1, 1, 2, 2, 2, 3, 7, 1, 1] 37 rigid atoms, others: [35, 36, 5, 7, 8, 9, 10, 11, 20, 28, 29] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074271 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074271 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074271/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074271 Building REAL250005074272 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074272' /scratch/stefan/7916156/working/building/REAL250005074272 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074272 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074272/0 /scratch/stefan/7916156/working/building/REAL250005074272 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 388) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/388 `/scratch/stefan/7916156/working/3D/388' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC=CC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074272.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074272/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074272 none COCC=CC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 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', '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, 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, 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] 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, 53, 53, 19, 10, 19, 10, 10, 6, 10, 6, 1, 6, 1, 1, 1, 1, 1, 1, 10, 96, 96, 96, 92, 92, 53, 53, 10, 10, 10, 10, 10, 7, 1, 10, 10] 96 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: 340 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074272 none COCC=CC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 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', '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, 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, 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] 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: [79, 71, 25, 25, 6, 1, 6, 1, 1, 1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 10, 1, 79, 79, 79, 71, 71, 25, 25, 1, 1, 2, 2, 2, 3, 10, 1, 1] 96 rigid atoms, others: [35, 36, 5, 7, 8, 9, 10, 11, 20, 28, 29] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34]) total number of confs: 282 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074272 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074272 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074272/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074272 Building REAL250005074273 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074273' /scratch/stefan/7916156/working/building/REAL250005074273 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074273 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074273/0 /scratch/stefan/7916156/working/building/REAL250005074273 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 389) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/389 `/scratch/stefan/7916156/working/3D/389' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(O)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074273.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074273/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074273 none CCC(C)(O)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 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', 'C.3', 'H', 'H', '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, 5, 7, 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, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 117 conformations in input total number of sets (complete confs): 117 using faster count positions algorithm for large data unique positions, atoms: [39, 36, 20, 36, 36, 10, 20, 10, 10, 7, 10, 7, 1, 7, 1, 1, 1, 1, 1, 1, 10, 39, 39, 39, 39, 39, 36, 36, 36, 108, 10, 10, 10, 10, 10, 8, 1, 10, 10] 117 rigid atoms, others: [36, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 259 number of broken/clashed sets: 50 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074273 none CCC(C)(O)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 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', 'C.3', 'H', 'H', '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, 5, 7, 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, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 117 conformations in input total number of sets (complete confs): 117 using faster count positions algorithm for large data unique positions, atoms: [26, 19, 5, 19, 19, 1, 5, 1, 1, 1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 10, 1, 28, 28, 28, 28, 28, 19, 19, 19, 57, 1, 1, 2, 2, 2, 3, 10, 1, 1] 117 rigid atoms, others: [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, 32, 33, 34, 35, 36]) total number of confs: 211 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074273 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074273 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074273/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074273 Building REAL250005074274 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074274' /scratch/stefan/7916156/working/building/REAL250005074274 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074274 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074274/0 /scratch/stefan/7916156/working/building/REAL250005074274 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 390) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/390 `/scratch/stefan/7916156/working/3D/390' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCC(C)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074274.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074274/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074274 none C#CCC(C)C(=O)N1CC(C)(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 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 45, 22, 45, 11, 22, 11, 11, 8, 11, 8, 1, 8, 1, 1, 1, 1, 1, 1, 11, 56, 56, 56, 45, 45, 45, 45, 11, 11, 11, 11, 11, 9, 1, 11, 11] 56 rigid atoms, others: [34, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36]) total number of confs: 226 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074274 none C#CCC(C)C(=O)N1CC(C)(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 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 23, 7, 23, 1, 7, 1, 1, 1, 1, 1, 3, 3, 3, 11, 11, 11, 11, 11, 1, 43, 43, 43, 23, 23, 23, 23, 1, 1, 2, 2, 2, 3, 11, 1, 1] 56 rigid atoms, others: [35, 36, 5, 7, 8, 9, 10, 11, 20, 28, 29] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34]) total number of confs: 193 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074274 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074274 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074274/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074274 Building REAL250005074275 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074275' /scratch/stefan/7916156/working/building/REAL250005074275 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074275 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074275/0 /scratch/stefan/7916156/working/building/REAL250005074275 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 391) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/391 `/scratch/stefan/7916156/working/3D/391' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(O)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074275.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074275/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074275 none C=CC(O)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 16, 31, 8, 16, 8, 8, 6, 8, 6, 1, 6, 1, 1, 1, 1, 1, 1, 8, 31, 31, 31, 31, 93, 8, 8, 8, 8, 8, 7, 1, 8, 8] 93 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33]) total number of confs: 202 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074275 none C=CC(O)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [23, 19, 6, 19, 1, 6, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 1, 23, 23, 23, 19, 57, 1, 1, 2, 2, 2, 3, 8, 1, 1] 93 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 19, 25, 26] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31]) total number of confs: 155 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074275 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074275 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074275/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074275 Building REAL250005074276 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074276' /scratch/stefan/7916156/working/building/REAL250005074276 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074276 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074276/0 /scratch/stefan/7916156/working/building/REAL250005074276 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 392) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/392 `/scratch/stefan/7916156/working/3D/392' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C23CC2CC3)C1) `REAL250005074276.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074276/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074276 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C23CC2CC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 10, 10, 10, 20, 20, 42, 42, 42, 42, 10, 10, 10, 10, 6, 1, 10, 10, 42, 42, 42, 42, 42, 42, 42, 10, 10] 42 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 25] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 96 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074276 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C23CC2CC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 10, 1, 1, 1, 6, 6, 23, 23, 23, 23, 1, 2, 2, 2, 3, 10, 1, 1, 23, 23, 23, 23, 23, 23, 23, 1, 1] 42 rigid atoms, others: [0, 1, 2, 35, 36, 11, 12, 13, 20, 26, 27] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34]) 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.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: REAL250005074276 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C23CC2CC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 37, 37, 37, 42, 42, 42, 42, 42, 23, 5, 1, 5, 1, 1, 1, 1, 1, 23, 23, 23, 23, 37, 42, 23, 23, 1, 1, 1, 1, 1, 1, 1, 23, 23] 42 rigid atoms, others: [32, 33, 34, 13, 15, 16, 17, 18, 19, 28, 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, 35, 36]) total number of confs: 98 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074276 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074276 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074276/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074276 Building REAL250005074277 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074277' /scratch/stefan/7916156/working/building/REAL250005074277 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074277 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074277/0 /scratch/stefan/7916156/working/building/REAL250005074277 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 393) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/393 `/scratch/stefan/7916156/working/3D/393' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C[C@H](C)CC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074277.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074277/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074277 none C=C[C@H](C)CC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 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', 'C.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, 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 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 56, 71, 71, 17, 7, 17, 7, 7, 6, 7, 6, 1, 6, 1, 1, 1, 1, 1, 1, 7, 71, 71, 71, 71, 71, 71, 56, 56, 7, 7, 7, 7, 7, 6, 1, 7, 7] 71 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: 270 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074277 none C=C[C@H](C)CC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 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', 'C.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, 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 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [62, 57, 36, 57, 57, 6, 1, 6, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 1, 62, 62, 62, 57, 57, 57, 36, 36, 1, 1, 2, 2, 2, 3, 7, 1, 1] 71 rigid atoms, others: [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, 32, 33, 34, 35, 36]) total number of confs: 260 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074277 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074277 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074277/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074277 Building REAL250005074278 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074278' /scratch/stefan/7916156/working/building/REAL250005074278 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074278 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074278/0 /scratch/stefan/7916156/working/building/REAL250005074278 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 394) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/394 `/scratch/stefan/7916156/working/3D/394' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C=CC2CC2)C1) `REAL250005074278.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074278/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074278 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C=CC2CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 91 conformations in input total number of sets (complete confs): 91 using faster count positions algorithm for large data unique positions, atoms: [14, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 14, 14, 14, 31, 31, 64, 64, 91, 91, 14, 14, 14, 14, 8, 1, 14, 14, 64, 64, 91, 91, 91, 91, 91, 14, 14] 91 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 25] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 301 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074278 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C=CC2CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 91 conformations in input total number of sets (complete confs): 91 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 3, 3, 3, 14, 14, 14, 14, 14, 1, 1, 1, 6, 6, 31, 31, 63, 63, 1, 2, 2, 2, 3, 14, 1, 1, 31, 31, 63, 63, 63, 63, 63, 1, 1] 91 rigid atoms, others: [0, 1, 2, 35, 36, 11, 12, 13, 20, 26, 27] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074278 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C=CC2CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 91 conformations in input total number of sets (complete confs): 91 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 84, 84, 84, 91, 91, 91, 91, 91, 63, 38, 8, 38, 8, 1, 1, 1, 1, 63, 64, 64, 64, 84, 91, 63, 63, 8, 8, 1, 1, 1, 1, 1, 63, 63] 91 rigid atoms, others: [32, 33, 34, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36]) total number of confs: 235 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074278 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074278 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074278/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074278 Building REAL250005074279 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074279' /scratch/stefan/7916156/working/building/REAL250005074279 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074279 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074279/0 /scratch/stefan/7916156/working/building/REAL250005074279 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 395) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/395 `/scratch/stefan/7916156/working/3D/395' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C#N)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074279.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074279.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074279/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074279 none CCC(C#N)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 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', 'C.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, 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 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [32, 31, 10, 31, 31, 6, 10, 6, 6, 5, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 34, 34, 34, 34, 34, 31, 6, 6, 6, 6, 6, 5, 1, 6, 6] 34 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: 144 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074279 none CCC(C#N)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 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', 'C.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, 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 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [24, 18, 5, 18, 18, 1, 5, 1, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 6, 1, 26, 26, 26, 26, 26, 18, 1, 1, 2, 2, 2, 3, 6, 1, 1] 34 rigid atoms, others: [34, 35, 5, 7, 8, 9, 10, 11, 20, 27, 28] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 135 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074279 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074279 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074279/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074279 Building REAL250005074280 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074280' /scratch/stefan/7916156/working/building/REAL250005074280 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074280 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074280/0 /scratch/stefan/7916156/working/building/REAL250005074280 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 396) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/396 `/scratch/stefan/7916156/working/3D/396' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2C3CCC32)C1) `REAL250005074280.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074280/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074280 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2C3CCC32)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 12, 12, 12, 24, 24, 44, 44, 44, 44, 12, 12, 12, 12, 7, 1, 12, 12, 44, 44, 44, 44, 44, 44, 44, 12, 12] 44 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 25] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 135 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074280 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2C3CCC32)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 3, 3, 3, 12, 12, 12, 12, 12, 1, 1, 1, 6, 6, 24, 24, 24, 24, 1, 2, 2, 2, 3, 12, 1, 1, 24, 24, 24, 24, 24, 24, 24, 1, 1] 44 rigid atoms, others: [0, 1, 2, 35, 36, 11, 12, 13, 20, 26, 27] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074280 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2C3CCC32)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 40, 40, 40, 44, 44, 44, 44, 44, 24, 7, 1, 7, 1, 1, 1, 1, 1, 24, 24, 24, 24, 40, 44, 24, 24, 1, 1, 1, 1, 1, 1, 1, 24, 24] 44 rigid atoms, others: [32, 33, 34, 13, 15, 16, 17, 18, 19, 28, 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, 35, 36]) total number of confs: 110 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074280 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074280 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074280/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074280 Building REAL250005074281 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074281' /scratch/stefan/7916156/working/building/REAL250005074281 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074281 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074281/0 /scratch/stefan/7916156/working/building/REAL250005074281 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 397) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/397 `/scratch/stefan/7916156/working/3D/397' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C1CCC1C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074281.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074281.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074281/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074281 none C=C1CCC1C(=O)N1CC(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'] 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 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 6, 1, 6, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 1, 20, 20, 20, 20, 20, 20, 20, 1, 1, 2, 2, 2, 2, 7, 1, 1] 28 rigid atoms, others: [35, 36, 5, 7, 8, 9, 10, 11, 20, 28, 29] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34]) total number of confs: 67 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074281 none C=C1CCC1C(=O)N1CC(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'] 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 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 8, 20, 20, 20, 20, 25, 25, 25, 28, 28, 28, 28, 28, 20, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 25, 28, 20, 20] 28 rigid atoms, others: [0, 1, 2, 3, 4, 5, 21, 22, 23, 24, 25, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36]) 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.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: REAL250005074281 none C=C1CCC1C(=O)N1CC(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'] 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 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 14, 7, 14, 7, 7, 6, 7, 6, 1, 6, 1, 1, 1, 1, 1, 1, 7, 28, 28, 28, 28, 28, 28, 28, 7, 7, 8, 8, 8, 6, 1, 7, 7] 28 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: 91 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074281 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074281 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074281/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074281 Building REAL250005074282 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074282' /scratch/stefan/7916156/working/building/REAL250005074282 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074282 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074282/0 /scratch/stefan/7916156/working/building/REAL250005074282 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 398) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/398 `/scratch/stefan/7916156/working/3D/398' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C(C(=O)N2CC(C)(NC(=O)C3=CC(=O)[N-]O3)C2)[C@H]1C) `REAL250005074282.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074282/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074282 none C[C@H]1C(C(=O)N2CC(C)(NC(=O)C3=CC(=O)[N-]O3)C2)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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: [23, 23, 23, 6, 1, 6, 1, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 6, 1, 23, 23, 23, 23, 23, 23, 23, 1, 1, 2, 2, 2, 3, 6, 1, 1, 23, 23, 23] 36 rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 10, 19, 27, 28] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 36, 37, 38]) total number of confs: 75 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074282 none C[C@H]1C(C(=O)N2CC(C)(NC(=O)C3=CC(=O)[N-]O3)C2)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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: [1, 1, 1, 1, 1, 8, 8, 23, 23, 23, 23, 30, 30, 30, 36, 36, 36, 36, 36, 23, 1, 1, 1, 2, 2, 2, 1, 23, 23, 23, 23, 23, 30, 36, 23, 23, 2, 2, 2] 36 rigid atoms, others: [0, 1, 2, 3, 4, 20, 21, 22, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 91 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.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: REAL250005074282 none C[C@H]1C(C(=O)N2CC(C)(NC(=O)C3=CC(=O)[N-]O3)C2)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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: [36, 36, 36, 14, 6, 14, 6, 6, 5, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 36, 36, 36, 36, 36, 36, 36, 6, 6, 6, 6, 6, 5, 1, 6, 6, 36, 36, 36] 36 rigid atoms, others: [33, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38]) total number of confs: 105 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074282 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074282 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074282/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074282 Building REAL250005074283 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074283' /scratch/stefan/7916156/working/building/REAL250005074283 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL250005074283 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074283/0 /scratch/stefan/7916156/working/building/REAL250005074283 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 399) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/399 `/scratch/stefan/7916156/working/3D/399' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@H+](C)CC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074283.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074283/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074283 none CC[N@H+](C)CC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 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', '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, 9, 6, 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, 6, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [30, 29, 26, 29, 29, 12, 9, 12, 9, 9, 7, 8, 7, 1, 7, 1, 1, 1, 1, 1, 1, 9, 30, 30, 30, 30, 30, 29, 29, 29, 26, 26, 9, 9, 9, 9, 9, 8, 1, 9, 9] 30 rigid atoms, others: [38, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40]) total number of confs: 125 number of broken/clashed sets: 28 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074283 none CC[N@H+](C)CC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 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', '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, 9, 6, 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, 6, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 19, 12, 19, 19, 3, 1, 3, 1, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 8, 1, 24, 24, 24, 24, 24, 19, 19, 19, 12, 12, 1, 1, 2, 2, 2, 2, 9, 1, 1] 30 rigid atoms, others: [32, 33, 6, 39, 8, 9, 10, 11, 12, 40, 21] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38]) total number of confs: 131 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074283 /scratch/stefan/7916156/working /scratch/stefan/7916156 mkdir: created directory `1' /scratch/stefan/7916156/working/building/REAL250005074283/1 /scratch/stefan/7916156/working/building/REAL250005074283 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 1 (index: 400) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/400 `/scratch/stefan/7916156/working/3D/400' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@@H+](C)CC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074283.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005074283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074283/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074283 none CC[N@@H+](C)CC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 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', '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, 9, 6, 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, 6, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 24, 27, 27, 11, 8, 11, 8, 8, 6, 8, 6, 1, 6, 1, 1, 1, 1, 1, 1, 8, 27, 27, 27, 27, 27, 27, 27, 27, 24, 24, 8, 8, 8, 8, 8, 7, 1, 8, 8] 27 rigid atoms, others: [38, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40]) total number of confs: 106 number of broken/clashed sets: 25 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074283 none CC[N@@H+](C)CC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 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', '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, 9, 6, 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, 6, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [22, 20, 13, 20, 20, 3, 1, 3, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 1, 22, 22, 22, 22, 22, 20, 20, 20, 13, 13, 1, 1, 2, 2, 2, 3, 8, 1, 1] 27 rigid atoms, others: [32, 33, 6, 39, 8, 9, 10, 11, 12, 40, 21] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38]) total number of confs: 112 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074283 /scratch/stefan/7916156/working /scratch/stefan/7916156 mkdir: created directory `2' /scratch/stefan/7916156/working/building/REAL250005074283/2 /scratch/stefan/7916156/working/building/REAL250005074283 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 2 (index: 401) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/401 `/scratch/stefan/7916156/working/3D/401' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)CC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074283.mol2' -> `2.mol2' `temp.mol2' -> `REAL250005074283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074283/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074283 none CCN(C)CC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 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', '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, 10, 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, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [74, 71, 55, 71, 19, 8, 19, 8, 8, 6, 8, 6, 1, 6, 1, 1, 1, 1, 1, 1, 8, 74, 74, 74, 74, 74, 71, 71, 71, 55, 55, 8, 8, 8, 8, 8, 6, 1, 8, 8] 74 rigid atoms, others: [37, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39]) total number of confs: 271 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074283 none CCN(C)CC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 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', '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, 10, 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, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [62, 56, 31, 56, 6, 1, 6, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 1, 62, 62, 62, 62, 62, 56, 56, 56, 31, 31, 1, 1, 2, 2, 2, 3, 8, 1, 1] 74 rigid atoms, others: [32, 5, 38, 7, 8, 9, 10, 11, 20, 39, 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, 30, 33, 34, 35, 36, 37]) total number of confs: 237 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074283 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074283 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 1: /scratch/stefan/7916156/working/building/REAL250005074283/1.* 2: /scratch/stefan/7916156/working/building/REAL250005074283/2.* 0: /scratch/stefan/7916156/working/building/REAL250005074283/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074283 Building REAL250005074284 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074284' /scratch/stefan/7916156/working/building/REAL250005074284 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074284 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074284/0 /scratch/stefan/7916156/working/building/REAL250005074284 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 402) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/402 `/scratch/stefan/7916156/working/3D/402' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074284.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074284/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074284 none CC(O)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [16, 9, 16, 6, 9, 6, 6, 4, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 6, 16, 16, 16, 16, 48, 6, 6, 6, 6, 6, 5, 1, 6, 6] 48 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: 108 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074284 none CC(O)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [9, 3, 9, 1, 3, 1, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 6, 1, 9, 9, 9, 9, 27, 1, 1, 2, 2, 2, 3, 6, 1, 1] 48 rigid atoms, others: [32, 3, 5, 6, 7, 8, 9, 18, 24, 25, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30]) total number of confs: 74 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074284 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074284 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074284/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074284 Building REAL250005074285 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074285' /scratch/stefan/7916156/working/building/REAL250005074285 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074285 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074285/0 /scratch/stefan/7916156/working/building/REAL250005074285 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 403) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/403 `/scratch/stefan/7916156/working/3D/403' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074285.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074285/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074285 none CC(=O)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 11, 8, 5, 5, 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, 3, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [21, 17, 21, 8, 17, 8, 8, 6, 8, 6, 1, 6, 1, 1, 1, 1, 1, 1, 8, 21, 21, 21, 8, 8, 8, 8, 8, 7, 1, 8, 8] 21 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30]) total number of confs: 67 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074285 none CC(=O)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 11, 8, 5, 5, 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, 3, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [15, 6, 15, 1, 6, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 1, 16, 16, 16, 1, 1, 2, 2, 2, 3, 8, 1, 1] 21 rigid atoms, others: [3, 5, 6, 7, 8, 9, 18, 22, 23, 29, 30] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 24, 25, 26, 27, 28]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074285 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074285 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074285/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074285 Building REAL250005074286 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074286' /scratch/stefan/7916156/working/building/REAL250005074286 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074286 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074286/0 /scratch/stefan/7916156/working/building/REAL250005074286 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 404) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/404 `/scratch/stefan/7916156/working/3D/404' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)CCCC#N)C1) `REAL250005074286.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074286/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074286 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)CCCC#N)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 1, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 12, 12, 12, 34, 34, 131, 151, 201, 201, 12, 12, 12, 12, 7, 1, 12, 12, 131, 131, 169, 169, 191, 192, 12, 12] 201 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 25] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 931 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074286 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)CCCC#N)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 1, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 3, 3, 3, 12, 12, 12, 12, 12, 1, 1, 1, 6, 6, 47, 64, 126, 126, 1, 2, 2, 2, 3, 12, 1, 1, 47, 47, 81, 81, 115, 117, 1, 1] 201 rigid atoms, others: [0, 1, 2, 34, 11, 12, 13, 35, 20, 26, 27] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33]) total number of confs: 631 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074286 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074286 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074286/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074286 Building REAL250005074287 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074287' /scratch/stefan/7916156/working/building/REAL250005074287 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074287 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074287/0 /scratch/stefan/7916156/working/building/REAL250005074287 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 405) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/405 `/scratch/stefan/7916156/working/3D/405' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2(C#N)CC2)C1) `REAL250005074287.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074287/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074287 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2(C#N)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 1, 8, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 12, 12, 20, 20, 20, 20, 7, 7, 7, 7, 5, 1, 7, 7, 20, 20, 20, 20, 7, 7] 20 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 25] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 59 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074287 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2(C#N)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 1, 8, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 3, 7, 7, 7, 7, 7, 1, 1, 1, 5, 5, 9, 9, 9, 9, 1, 2, 2, 2, 3, 7, 1, 1, 9, 9, 9, 9, 1, 1] 20 rigid atoms, others: [0, 1, 2, 33, 32, 11, 12, 13, 20, 26, 27] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30, 31]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074287 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2(C#N)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 1, 8, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 18, 18, 18, 20, 20, 20, 20, 20, 9, 4, 1, 4, 1, 1, 1, 1, 1, 9, 10, 10, 10, 18, 20, 9, 9, 1, 1, 1, 1, 9, 9] 20 rigid atoms, others: [13, 15, 16, 17, 18, 19, 28, 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, 32, 33]) total number of confs: 59 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074287 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074287 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074287/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074287 Building REAL250005074288 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074288' /scratch/stefan/7916156/working/building/REAL250005074288 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074288 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074288/0 /scratch/stefan/7916156/working/building/REAL250005074288 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 406) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/406 `/scratch/stefan/7916156/working/3D/406' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C1CC(C(=O)N2CC(C)(NC(=O)C3=CC(=O)[N-]O3)C2)C1) `REAL250005074288.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074288/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074288 none C=C1CC(C(=O)N2CC(C)(NC(=O)C3=CC(=O)[N-]O3)C2)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', '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, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 6, 1, 6, 1, 1, 1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 10, 1, 19, 19, 19, 19, 19, 19, 1, 1, 2, 2, 2, 3, 10, 1, 1, 19, 19] 31 rigid atoms, others: [33, 34, 4, 6, 7, 8, 9, 10, 19, 26, 27] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 35, 36]) total number of confs: 67 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074288 none C=C1CC(C(=O)N2CC(C)(NC(=O)C3=CC(=O)[N-]O3)C2)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', '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, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 8, 8, 19, 19, 19, 19, 26, 26, 26, 31, 31, 31, 31, 31, 19, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 26, 31, 19, 19, 1, 1] 31 rigid atoms, others: [0, 1, 2, 3, 4, 35, 20, 21, 22, 23, 24, 25, 36] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074288 none C=C1CC(C(=O)N2CC(C)(NC(=O)C3=CC(=O)[N-]O3)C2)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', '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, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 19, 10, 19, 10, 10, 8, 10, 8, 1, 8, 1, 1, 1, 1, 1, 1, 10, 31, 31, 31, 31, 31, 31, 10, 10, 10, 10, 10, 8, 1, 10, 10, 31, 31] 31 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: 87 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074288 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074288 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074288/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074288 Building REAL250005074289 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074289' /scratch/stefan/7916156/working/building/REAL250005074289 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074289 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074289/0 /scratch/stefan/7916156/working/building/REAL250005074289 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 407) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/407 `/scratch/stefan/7916156/working/3D/407' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2(F)CC2)C1) `REAL250005074289.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074289/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074289 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2(F)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 15, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [11, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 11, 11, 11, 24, 24, 38, 38, 38, 11, 11, 11, 11, 7, 1, 11, 11, 38, 38, 38, 38, 11, 11] 38 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 24] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 119 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074289 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2(F)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 15, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 3, 3, 3, 11, 11, 11, 11, 11, 1, 1, 1, 6, 6, 24, 24, 24, 1, 2, 2, 2, 3, 11, 1, 1, 24, 24, 24, 24, 1, 1] 38 rigid atoms, others: [0, 1, 2, 32, 11, 12, 13, 19, 25, 26, 31] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 27, 28, 29, 30]) 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.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: REAL250005074289 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2(F)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 15, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 32, 32, 32, 38, 38, 38, 38, 38, 24, 9, 1, 9, 1, 1, 1, 1, 24, 24, 24, 24, 32, 38, 24, 24, 1, 1, 1, 1, 24, 24] 38 rigid atoms, others: [13, 15, 16, 17, 18, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32]) total number of confs: 85 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074289 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074289 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074289/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074289 Building REAL250005074290 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074290' /scratch/stefan/7916156/working/building/REAL250005074290 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074290 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074290/0 /scratch/stefan/7916156/working/building/REAL250005074290 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 408) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/408 `/scratch/stefan/7916156/working/3D/408' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)(C)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074290.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074290/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074290 none COC(C)(C)C(=O)N1CC(C)(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 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 18, 11, 18, 18, 5, 11, 5, 5, 3, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 19, 19, 19, 18, 18, 18, 18, 18, 18, 5, 5, 5, 5, 5, 3, 1, 5, 5] 19 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: 66 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074290 none COC(C)(C)C(=O)N1CC(C)(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 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [17, 13, 7, 13, 13, 1, 7, 1, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 5, 1, 17, 17, 17, 13, 13, 13, 13, 13, 13, 1, 1, 2, 2, 2, 3, 5, 1, 1] 19 rigid atoms, others: [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, 32, 33, 34, 35, 36]) total number of confs: 64 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074290 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074290 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074290/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074290 Building REAL250005074291 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074291' /scratch/stefan/7916156/working/building/REAL250005074291 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074291 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074291/0 /scratch/stefan/7916156/working/building/REAL250005074291 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 409) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/409 `/scratch/stefan/7916156/working/3D/409' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC#N)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074291.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074291.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074291/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074291 none CC(CC#N)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 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', 'C.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, 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 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [27, 15, 27, 34, 34, 8, 15, 8, 8, 7, 8, 7, 1, 7, 1, 1, 1, 1, 1, 1, 8, 27, 27, 27, 27, 34, 34, 8, 8, 8, 8, 8, 7, 1, 8, 8] 34 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: 128 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074291 none CC(CC#N)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 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', 'C.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, 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 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [19, 6, 19, 30, 30, 1, 6, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 1, 19, 19, 19, 19, 30, 30, 1, 1, 2, 2, 2, 3, 8, 1, 1] 34 rigid atoms, others: [34, 35, 5, 7, 8, 9, 10, 11, 20, 27, 28] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 139 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074291 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074291 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074291/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074291 Building REAL250005074292 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074292' /scratch/stefan/7916156/working/building/REAL250005074292 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074292 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074292/0 /scratch/stefan/7916156/working/building/REAL250005074292 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 410) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/410 `/scratch/stefan/7916156/working/3D/410' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1CC1C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074292.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074292/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074292 none CCC1CC1C(=O)N1CC(C)(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 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [20, 19, 19, 19, 5, 1, 5, 1, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 8, 1, 20, 20, 20, 20, 20, 19, 19, 19, 19, 1, 1, 2, 2, 2, 2, 8, 1, 1] 29 rigid atoms, others: [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, 32, 33, 34, 35, 36]) total number of confs: 70 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074292 none CCC1CC1C(=O)N1CC(C)(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 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, 8, 8, 19, 19, 19, 19, 24, 24, 24, 29, 29, 29, 29, 29, 19, 3, 3, 3, 3, 3, 1, 1, 1, 1, 19, 19, 19, 19, 19, 24, 29, 19, 19] 29 rigid atoms, others: [1, 2, 3, 4, 5, 26, 27, 28, 29] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38]) 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.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: REAL250005074292 none CCC1CC1C(=O)N1CC(C)(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 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 18, 8, 18, 8, 8, 7, 8, 7, 1, 7, 1, 1, 1, 1, 1, 1, 8, 29, 29, 29, 29, 29, 29, 29, 29, 29, 8, 8, 9, 9, 9, 7, 1, 8, 8] 29 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: 87 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074292 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074292 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074292/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074292 Building REAL250005074293 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074293' /scratch/stefan/7916156/working/building/REAL250005074293 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074293 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074293/0 /scratch/stefan/7916156/working/building/REAL250005074293 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 411) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/411 `/scratch/stefan/7916156/working/3D/411' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(C)(O)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074293.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074293/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074293 none C=CC(C)(O)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 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', '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, 12, 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, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 17, 30, 30, 8, 17, 8, 8, 6, 8, 6, 1, 6, 1, 1, 1, 1, 1, 1, 8, 30, 30, 30, 30, 30, 30, 90, 8, 8, 8, 8, 8, 7, 1, 8, 8] 90 rigid atoms, others: [34, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36]) total number of confs: 200 number of broken/clashed sets: 21 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074293 none C=CC(C)(O)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 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', '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, 12, 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, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [23, 19, 6, 19, 19, 1, 6, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 1, 23, 23, 23, 19, 19, 19, 57, 1, 1, 2, 2, 2, 3, 8, 1, 1] 90 rigid atoms, others: [35, 36, 5, 7, 8, 9, 10, 11, 20, 28, 29] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34]) total number of confs: 158 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074293 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074293 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074293/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074293 Building REAL250005074294 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074294' /scratch/stefan/7916156/working/building/REAL250005074294 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074294 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074294/0 /scratch/stefan/7916156/working/building/REAL250005074294 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 412) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/412 `/scratch/stefan/7916156/working/3D/412' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC=CC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074294.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074294.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074294/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074294 none CCCC=CC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 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 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [111, 101, 68, 68, 21, 9, 21, 9, 9, 7, 9, 7, 1, 7, 1, 1, 1, 1, 1, 1, 9, 111, 111, 111, 111, 111, 101, 101, 68, 68, 9, 9, 9, 9, 9, 8, 1, 9, 9] 111 rigid atoms, others: [36, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 416 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074294 none CCCC=CC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 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 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [89, 76, 33, 33, 6, 1, 6, 1, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 1, 90, 90, 90, 90, 90, 76, 76, 33, 33, 1, 1, 2, 2, 2, 3, 9, 1, 1] 111 rigid atoms, others: [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, 32, 33, 34, 35, 36]) total number of confs: 375 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074294 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074294 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074294/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074294 Building REAL250005074295 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074295' /scratch/stefan/7916156/working/building/REAL250005074295 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074295 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074295/0 /scratch/stefan/7916156/working/building/REAL250005074295 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 413) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/413 `/scratch/stefan/7916156/working/3D/413' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=C(F)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074295.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074295/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074295 none CC=C(F)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 16, 22, 8, 16, 8, 8, 6, 8, 6, 1, 6, 1, 1, 1, 1, 1, 1, 8, 22, 22, 22, 22, 8, 8, 8, 8, 8, 7, 1, 8, 8] 22 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32]) total number of confs: 67 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074295 none CC=C(F)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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: [15, 15, 5, 15, 1, 5, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 1, 16, 16, 16, 15, 1, 1, 2, 2, 2, 3, 8, 1, 1] 22 rigid atoms, others: [32, 4, 6, 7, 8, 9, 10, 19, 24, 25, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 26, 27, 28, 29, 30]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074295 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074295 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074295/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074295 Building REAL250005074296 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074296' /scratch/stefan/7916156/working/building/REAL250005074296 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005074296 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074296/0 /scratch/stefan/7916156/working/building/REAL250005074296 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 414) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/414 `/scratch/stefan/7916156/working/3D/414' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1)[NH+](C)C) `REAL250005074296.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074296/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074296 none C[C@H](C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1)[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', '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, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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, 5, 6, 3, 5, 3, 3, 2, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 6, 6, 6, 6, 6, 6, 6, 3, 3, 3, 3, 3, 2, 1, 3, 3, 6, 6, 6, 6, 6, 6] 6 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, 39, 40]) total number of confs: 21 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074296 none C[C@H](C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1)[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', '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, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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: [5, 4, 5, 1, 4, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 3, 1, 5, 6, 6, 6, 5, 5, 5, 1, 1, 2, 2, 2, 2, 3, 1, 1, 6, 6, 6, 6, 6, 6] 6 rigid atoms, others: [33, 34, 3, 5, 6, 7, 8, 9, 18, 26, 27] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40]) total number of confs: 33 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074296 /scratch/stefan/7916156/working /scratch/stefan/7916156 mkdir: created directory `1' /scratch/stefan/7916156/working/building/REAL250005074296/1 /scratch/stefan/7916156/working/building/REAL250005074296 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 1 (index: 415) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/415 `/scratch/stefan/7916156/working/3D/415' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1)N(C)C) `REAL250005074296.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005074296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074296/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074296 none C[C@H](C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', '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, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 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 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [17, 11, 17, 6, 11, 6, 6, 4, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 17, 18, 18, 17, 17, 17, 6, 6, 6, 6, 6, 4, 1, 6, 5, 18, 18, 18, 18, 18, 18] 18 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 68 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074296 none C[C@H](C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', '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, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 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 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [13, 5, 13, 1, 5, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 1, 13, 17, 17, 13, 13, 13, 1, 1, 2, 2, 2, 2, 5, 1, 1, 17, 17, 17, 17, 17, 17] 18 rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 18, 25, 26] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39]) total number of confs: 72 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074296 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074296 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 1: /scratch/stefan/7916156/working/building/REAL250005074296/1.* 0: /scratch/stefan/7916156/working/building/REAL250005074296/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074296 Building REAL250005074297 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074297' /scratch/stefan/7916156/working/building/REAL250005074297 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074297 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074297/0 /scratch/stefan/7916156/working/building/REAL250005074297 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 416) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/416 `/scratch/stefan/7916156/working/3D/416' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC=CC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074297.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074297/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074297 none CCOC=CC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 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, 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 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [67, 64, 41, 41, 15, 8, 15, 8, 8, 6, 8, 6, 1, 6, 1, 1, 1, 1, 1, 1, 8, 67, 67, 67, 67, 67, 41, 41, 8, 8, 8, 8, 8, 7, 1, 8, 8] 67 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: 166 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074297 none CCOC=CC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 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, 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 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [58, 50, 23, 23, 5, 1, 5, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 1, 59, 59, 59, 58, 58, 23, 23, 1, 1, 2, 2, 2, 3, 8, 1, 1] 67 rigid atoms, others: [35, 36, 5, 7, 8, 9, 10, 11, 20, 28, 29] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074297 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074297 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074297/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074297 Building REAL250005074298 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074298' /scratch/stefan/7916156/working/building/REAL250005074298 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074298 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074298/0 /scratch/stefan/7916156/working/building/REAL250005074298 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 417) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/417 `/scratch/stefan/7916156/working/3D/417' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)OCC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074298.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074298/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074298 none CC(=O)OCC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 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', 'C.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, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 5, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 111, 22, 9, 22, 9, 9, 7, 9, 7, 1, 7, 1, 1, 1, 1, 1, 1, 9, 139, 139, 139, 111, 111, 9, 9, 9, 9, 9, 7, 1, 9, 9] 139 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: 437 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074298 none CC(=O)OCC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 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', 'C.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, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 5, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [108, 105, 108, 49, 6, 1, 6, 1, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 1, 109, 109, 109, 49, 49, 1, 1, 2, 2, 2, 3, 9, 1, 1] 139 rigid atoms, others: [33, 34, 5, 7, 8, 9, 10, 11, 20, 26, 27] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32]) total number of confs: 280 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074298 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074298 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074298/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074298 Building REAL250005074299 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074299' /scratch/stefan/7916156/working/building/REAL250005074299 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074299 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074299/0 /scratch/stefan/7916156/working/building/REAL250005074299 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 418) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/418 `/scratch/stefan/7916156/working/3D/418' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)C=CC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074299.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074299/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074299 none CC(=O)C=CC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 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', 'C.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, 5, 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] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [34, 25, 34, 25, 17, 8, 17, 8, 8, 6, 8, 6, 1, 6, 1, 1, 1, 1, 1, 1, 8, 34, 34, 34, 25, 25, 8, 8, 8, 8, 8, 7, 1, 8, 8] 34 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: 103 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074299 none CC(=O)C=CC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 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', 'C.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, 5, 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] 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: [27, 18, 27, 18, 6, 1, 6, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 1, 28, 28, 28, 18, 18, 1, 1, 2, 2, 2, 3, 8, 1, 1] 34 rigid atoms, others: [33, 34, 5, 7, 8, 9, 10, 11, 20, 26, 27] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074299 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074299 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074299/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074299 Building REAL250005074300 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074300' /scratch/stefan/7916156/working/building/REAL250005074300 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074300 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074300/0 /scratch/stefan/7916156/working/building/REAL250005074300 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 419) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/419 `/scratch/stefan/7916156/working/3D/419' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)COC2CC2)C1) `REAL250005074300.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074300/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074300 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)COC2CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [13, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 13, 13, 13, 34, 34, 120, 160, 180, 180, 13, 13, 13, 13, 7, 1, 13, 13, 120, 120, 180, 180, 180, 180, 180, 13, 13] 180 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 25] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 577 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074300 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)COC2CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 180 conformations in input total number of sets (complete confs): 180 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 3, 3, 3, 13, 13, 13, 13, 13, 1, 1, 1, 6, 6, 42, 112, 150, 150, 1, 2, 2, 2, 3, 13, 1, 1, 42, 42, 150, 150, 150, 150, 150, 1, 1] 180 rigid atoms, others: [0, 1, 2, 35, 36, 11, 12, 13, 20, 26, 27] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 400 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074300 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)COC2CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [150, 150, 150, 175, 175, 175, 180, 180, 180, 180, 180, 150, 104, 26, 104, 7, 1, 1, 1, 1, 150, 150, 150, 150, 175, 180, 150, 150, 26, 26, 1, 1, 1, 1, 1, 150, 150] 180 rigid atoms, others: [32, 33, 34, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36]) total number of confs: 468 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074300 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074300 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074300/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074300 Building REAL250005074301 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074301' /scratch/stefan/7916156/working/building/REAL250005074301 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074301 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074301/0 /scratch/stefan/7916156/working/building/REAL250005074301 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 420) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/420 `/scratch/stefan/7916156/working/3D/420' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=NC=CN2)C1) `REAL250005074301.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074301/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074301 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=NC=CN2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 8, 1, 1, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [10, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 10, 10, 10, 17, 17, 21, 21, 21, 21, 10, 10, 10, 10, 8, 1, 10, 10, 21, 21, 21, 10, 10] 21 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 25] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 57 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074301 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=NC=CN2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 8, 1, 1, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 10, 1, 1, 1, 6, 6, 15, 15, 15, 15, 1, 2, 2, 2, 3, 10, 1, 1, 15, 15, 15, 1, 1] 21 rigid atoms, others: [0, 1, 2, 32, 11, 12, 13, 20, 26, 27, 31] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30]) total number of confs: 47 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.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: REAL250005074301 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=NC=CN2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 8, 1, 1, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 13, 13, 22, 22, 22, 25, 25, 25, 25, 25, 13, 8, 1, 8, 1, 1, 1, 1, 1, 13, 14, 14, 14, 22, 25, 13, 13, 1, 1, 1, 13, 13] 25 rigid atoms, others: [13, 15, 16, 17, 18, 19, 28, 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, 31, 32]) total number of confs: 71 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074301 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074301 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074301/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074301 Building REAL250005074302 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074302' /scratch/stefan/7916156/working/building/REAL250005074302 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074302 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074302/0 /scratch/stefan/7916156/working/building/REAL250005074302 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 421) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/421 `/scratch/stefan/7916156/working/3D/421' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CO)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074302.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074302/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074302 none CC(CO)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 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 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [15, 9, 15, 17, 5, 9, 5, 5, 3, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 15, 17, 17, 51, 5, 5, 5, 5, 5, 3, 1, 5, 5] 51 rigid atoms, others: [33, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35]) total number of confs: 123 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074302 none CC(CO)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 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 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [9, 4, 9, 16, 1, 4, 1, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 5, 1, 9, 9, 9, 9, 16, 16, 48, 1, 1, 2, 2, 2, 3, 5, 1, 1] 51 rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 10, 19, 27, 28] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074302 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074302 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074302/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074302 Building REAL250005074303 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074303' /scratch/stefan/7916156/working/building/REAL250005074303 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074303 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074303/0 /scratch/stefan/7916156/working/building/REAL250005074303 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 422) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/422 `/scratch/stefan/7916156/working/3D/422' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=CON=C2)C1) `REAL250005074303.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074303/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074303 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=CON=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 1, 12, 8, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [11, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 11, 11, 11, 21, 21, 58, 58, 58, 58, 11, 11, 11, 11, 6, 1, 11, 11, 58, 58, 11, 11] 58 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 25] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31]) total number of confs: 119 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074303 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=CON=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 1, 12, 8, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 3, 3, 3, 11, 11, 11, 11, 11, 1, 1, 1, 6, 6, 34, 34, 34, 34, 1, 2, 2, 2, 3, 11, 1, 1, 34, 34, 1, 1] 58 rigid atoms, others: [0, 1, 2, 11, 12, 13, 20, 26, 27, 30, 31] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29]) total number of confs: 69 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.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: REAL250005074303 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=CON=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 1, 12, 8, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [34, 34, 34, 54, 54, 54, 58, 58, 58, 58, 58, 34, 9, 1, 9, 1, 1, 1, 1, 1, 34, 34, 34, 34, 54, 58, 34, 34, 1, 1, 34, 34] 58 rigid atoms, others: [13, 15, 16, 17, 18, 19, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31]) total number of confs: 140 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074303 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074303 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074303/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074303 Building REAL250005074304 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074304' /scratch/stefan/7916156/working/building/REAL250005074304 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074304 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074304/0 /scratch/stefan/7916156/working/building/REAL250005074304 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 423) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/423 `/scratch/stefan/7916156/working/3D/423' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)CCCCO)C1) `REAL250005074304.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074304/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074304 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)CCCCO)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 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: [10, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 10, 10, 10, 28, 28, 97, 134, 195, 199, 10, 10, 10, 10, 7, 1, 10, 10, 97, 97, 151, 151, 198, 197, 201, 201, 597, 10, 10] 603 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 25] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 1605 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074304 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)CCCCO)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 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: [1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 10, 1, 1, 1, 6, 6, 36, 51, 91, 143, 1, 2, 2, 2, 3, 10, 1, 1, 36, 36, 63, 63, 92, 92, 145, 145, 429, 1, 1] 603 rigid atoms, others: [0, 1, 2, 37, 38, 11, 12, 13, 20, 26, 27] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 1209 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074304 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074304 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074304/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074304 Building REAL250005074305 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074305' /scratch/stefan/7916156/working/building/REAL250005074305 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074305 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074305/0 /scratch/stefan/7916156/working/building/REAL250005074305 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 424) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/424 `/scratch/stefan/7916156/working/3D/424' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C(=O)C2CC2)C1) `REAL250005074305.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074305/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074305 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C(=O)C2CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 11, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [12, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 12, 12, 12, 32, 32, 68, 68, 102, 102, 12, 12, 12, 12, 7, 1, 12, 12, 102, 102, 102, 102, 102, 12, 12] 102 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 25] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 311 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074305 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C(=O)C2CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 11, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 3, 3, 3, 12, 12, 12, 12, 12, 1, 1, 1, 6, 6, 26, 26, 69, 69, 1, 2, 2, 2, 3, 12, 1, 1, 69, 69, 69, 69, 69, 1, 1] 102 rigid atoms, others: [0, 1, 2, 34, 33, 11, 12, 13, 20, 26, 27] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.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: REAL250005074305 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C(=O)C2CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 11, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [72, 72, 72, 99, 99, 99, 101, 101, 101, 101, 101, 72, 43, 13, 43, 1, 13, 1, 1, 1, 72, 72, 72, 72, 99, 101, 72, 72, 1, 1, 1, 1, 1, 72, 72] 101 rigid atoms, others: [32, 15, 17, 18, 19, 28, 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, 33, 34]) total number of confs: 269 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074305 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074305 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074305/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074305 Building REAL250005074306 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074306' /scratch/stefan/7916156/working/building/REAL250005074306 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074306 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074306/0 /scratch/stefan/7916156/working/building/REAL250005074306 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 425) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/425 `/scratch/stefan/7916156/working/3D/425' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)CC2(O)CC2)C1) `REAL250005074306.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074306/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074306 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)CC2(O)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 273 conformations in input total number of sets (complete confs): 273 using faster count positions algorithm for large data unique positions, atoms: [13, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 13, 13, 13, 28, 28, 70, 91, 91, 91, 13, 13, 13, 13, 6, 1, 13, 13, 70, 70, 273, 91, 91, 91, 91, 13, 13] 273 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 25] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 611 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074306 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)CC2(O)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 273 conformations in input total number of sets (complete confs): 273 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 3, 3, 3, 13, 13, 13, 13, 13, 1, 1, 1, 6, 6, 32, 60, 60, 60, 1, 2, 2, 2, 3, 13, 1, 1, 32, 32, 180, 60, 60, 60, 60, 1, 1] 273 rigid atoms, others: [0, 1, 2, 35, 36, 11, 12, 13, 20, 26, 27] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 411 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.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: REAL250005074306 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)CC2(O)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 273 conformations in input total number of sets (complete confs): 273 using faster count positions algorithm for large data unique positions, atoms: [60, 60, 60, 85, 85, 85, 91, 91, 91, 91, 91, 60, 28, 9, 28, 1, 1, 1, 1, 1, 60, 60, 60, 60, 85, 91, 60, 60, 9, 9, 6, 1, 1, 1, 1, 60, 60] 273 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]) total number of confs: 247 number of broken/clashed sets: 6 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074306 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074306 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074306/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074306 Building REAL250005074307 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074307' /scratch/stefan/7916156/working/building/REAL250005074307 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074307 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074307/0 /scratch/stefan/7916156/working/building/REAL250005074307 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 426) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/426 `/scratch/stefan/7916156/working/3D/426' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2CCC2F)C1) `REAL250005074307.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074307/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074307 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2CCC2F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 15, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [14, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 14, 14, 14, 32, 32, 58, 58, 58, 58, 14, 14, 14, 14, 8, 1, 14, 14, 58, 58, 58, 58, 58, 58, 14, 14] 58 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 25] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 181 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074307 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2CCC2F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 15, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 3, 3, 3, 14, 14, 14, 14, 14, 1, 1, 1, 6, 6, 28, 28, 28, 28, 1, 2, 2, 2, 3, 14, 1, 1, 28, 28, 28, 28, 28, 28, 1, 1] 58 rigid atoms, others: [0, 1, 2, 34, 11, 12, 13, 35, 20, 26, 27] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33]) 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.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: REAL250005074307 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2CCC2F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 15, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 46, 46, 46, 58, 58, 58, 58, 58, 28, 8, 1, 8, 1, 1, 1, 1, 1, 28, 28, 28, 28, 46, 58, 28, 28, 1, 1, 1, 1, 1, 1, 28, 28] 58 rigid atoms, others: [32, 33, 13, 15, 16, 17, 18, 19, 28, 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, 34, 35]) total number of confs: 138 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074307 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074307 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074307/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074307 Building REAL250005074308 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074308' /scratch/stefan/7916156/working/building/REAL250005074308 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074308 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074308/0 /scratch/stefan/7916156/working/building/REAL250005074308 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 427) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/427 `/scratch/stefan/7916156/working/3D/427' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)[C@@H]2C[C@H]2CF)C1) `REAL250005074308.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074308/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074308 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)[C@@H]2C[C@H]2CF)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 15, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [15, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 15, 15, 15, 35, 35, 86, 86, 86, 86, 86, 93, 15, 15, 15, 15, 9, 1, 15, 15, 86, 86, 93, 93, 15, 15] 93 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 27] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 287 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074308 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)[C@@H]2C[C@H]2CF)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 15, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 3, 3, 3, 15, 15, 15, 15, 15, 1, 1, 1, 6, 6, 33, 33, 33, 33, 33, 73, 1, 2, 2, 2, 3, 15, 1, 1, 33, 33, 73, 73, 1, 1] 93 rigid atoms, others: [0, 1, 2, 34, 11, 12, 13, 35, 22, 28, 29] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 30, 31, 32, 33]) 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.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: REAL250005074308 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)[C@@H]2C[C@H]2CF)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 15, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 33, 52, 52, 52, 86, 86, 86, 86, 86, 33, 9, 1, 9, 1, 1, 1, 1, 1, 1, 10, 33, 33, 33, 33, 52, 86, 33, 33, 1, 1, 10, 10, 33, 33] 93 rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35]) total number of confs: 211 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074308 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074308 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074308/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074308 Building REAL250005074309 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074309' /scratch/stefan/7916156/working/building/REAL250005074309 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074309 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074309/0 /scratch/stefan/7916156/working/building/REAL250005074309 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 428) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/428 `/scratch/stefan/7916156/working/3D/428' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CO)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074309.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074309/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074309 none CCC(CO)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 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', 'C.3', 'H', 'H', '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, 5, 7, 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, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [43, 33, 18, 33, 47, 9, 18, 9, 9, 6, 9, 6, 1, 6, 1, 1, 1, 1, 1, 1, 9, 45, 45, 45, 45, 45, 33, 47, 47, 141, 9, 9, 9, 9, 9, 7, 1, 9, 9] 141 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: 415 number of broken/clashed sets: 20 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074309 none CCC(CO)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 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', 'C.3', 'H', 'H', '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, 5, 7, 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, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [27, 18, 5, 18, 37, 1, 5, 1, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 1, 30, 30, 30, 30, 30, 18, 37, 37, 111, 1, 1, 2, 2, 2, 3, 9, 1, 1] 141 rigid atoms, others: [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, 32, 33, 34, 35, 36]) total number of confs: 370 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074309 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074309 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074309/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074309 Building REAL250005074310 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074310' /scratch/stefan/7916156/working/building/REAL250005074310 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074310 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074310/0 /scratch/stefan/7916156/working/building/REAL250005074310 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 429) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/429 `/scratch/stefan/7916156/working/3D/429' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)[C@@H]2C[C@@H]2C#N)C1) `REAL250005074310.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074310/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074310 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)[C@@H]2C[C@@H]2C#N)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 9, 9, 9, 19, 19, 25, 25, 25, 25, 25, 25, 9, 9, 9, 9, 6, 1, 9, 9, 25, 25, 9, 9] 25 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 27] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33]) total number of confs: 75 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074310 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)[C@@H]2C[C@@H]2C#N)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 1, 1, 1, 5, 5, 17, 17, 17, 17, 17, 17, 1, 2, 2, 2, 3, 9, 1, 1, 17, 17, 1, 1] 25 rigid atoms, others: [0, 1, 2, 33, 32, 11, 12, 13, 22, 28, 29] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 30, 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.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: REAL250005074310 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)[C@@H]2C[C@@H]2C#N)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 24, 24, 24, 25, 25, 25, 25, 25, 17, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 24, 25, 17, 17, 1, 1, 17, 17] 25 rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33]) total number of confs: 60 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074310 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074310 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074310/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074310 Building REAL250005074311 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074311' /scratch/stefan/7916156/working/building/REAL250005074311 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074311 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074311/0 /scratch/stefan/7916156/working/building/REAL250005074311 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 430) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/430 `/scratch/stefan/7916156/working/3D/430' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=COCC2)C1) `REAL250005074311.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074311/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074311 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=COCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 1, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 13, 13, 13, 30, 30, 49, 49, 49, 49, 13, 13, 13, 13, 7, 1, 13, 13, 49, 49, 49, 49, 49, 13, 13] 49 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 25] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 118 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074311 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=COCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 1, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 3, 3, 3, 13, 13, 13, 13, 13, 1, 1, 1, 6, 6, 27, 27, 27, 27, 1, 2, 2, 2, 3, 13, 1, 1, 27, 27, 27, 27, 27, 1, 1] 49 rigid atoms, others: [0, 1, 2, 34, 33, 11, 12, 13, 20, 26, 27] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074311 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=COCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 1, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 42, 42, 42, 49, 49, 49, 49, 49, 27, 12, 1, 12, 1, 1, 1, 1, 1, 27, 27, 27, 27, 42, 49, 27, 27, 1, 1, 1, 1, 1, 27, 27] 49 rigid atoms, others: [32, 13, 15, 16, 17, 18, 19, 28, 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, 33, 34]) total number of confs: 123 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074311 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074311 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074311/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074311 Building REAL250005074312 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074312' /scratch/stefan/7916156/working/building/REAL250005074312 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074312 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074312/0 /scratch/stefan/7916156/working/building/REAL250005074312 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 431) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/431 `/scratch/stefan/7916156/working/3D/431' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2(O)CC2)C1) `REAL250005074312.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074312/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074312 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2(O)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [11, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 11, 11, 11, 20, 20, 35, 35, 35, 11, 11, 11, 11, 6, 1, 11, 11, 105, 35, 35, 35, 35, 11, 11] 105 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 24] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 212 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074312 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2(O)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 3, 3, 3, 11, 11, 11, 11, 11, 1, 1, 1, 7, 7, 22, 22, 22, 1, 2, 2, 2, 3, 11, 1, 1, 66, 22, 22, 22, 22, 1, 1] 105 rigid atoms, others: [0, 1, 2, 33, 32, 11, 12, 13, 19, 25, 26] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31]) total number of confs: 141 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.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: REAL250005074312 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2(O)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 28, 28, 28, 35, 35, 35, 35, 35, 22, 9, 1, 9, 1, 1, 1, 1, 22, 22, 22, 22, 28, 35, 22, 22, 6, 1, 1, 1, 1, 22, 22] 105 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]) total number of confs: 83 number of broken/clashed sets: 8 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074312 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074312 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074312/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074312 Building REAL250005074313 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074313' /scratch/stefan/7916156/working/building/REAL250005074313 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074313 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074313/0 /scratch/stefan/7916156/working/building/REAL250005074313 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 432) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/432 `/scratch/stefan/7916156/working/3D/432' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=CCC2)C1) `REAL250005074313.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074313/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074313 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [12, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 12, 12, 12, 24, 24, 24, 24, 24, 12, 12, 12, 12, 8, 1, 12, 12, 24, 24, 24, 24, 24, 12, 12] 24 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 24] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 71 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074313 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 3, 3, 3, 12, 12, 12, 12, 12, 1, 1, 1, 6, 6, 20, 19, 20, 1, 2, 2, 2, 3, 12, 1, 1, 20, 20, 20, 20, 20, 1, 1] 24 rigid atoms, others: [0, 1, 2, 33, 32, 11, 12, 13, 19, 25, 26] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31]) 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.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: REAL250005074313 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 21, 21, 21, 24, 24, 24, 24, 24, 20, 11, 1, 11, 1, 1, 1, 1, 20, 20, 20, 20, 21, 24, 20, 20, 1, 1, 1, 1, 1, 20, 20] 24 rigid atoms, others: [13, 15, 16, 17, 18, 27, 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, 32, 33]) total number of confs: 49 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074313 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074313 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074313/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074313 Building REAL250005074314 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074314' /scratch/stefan/7916156/working/building/REAL250005074314 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074314 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074314/0 /scratch/stefan/7916156/working/building/REAL250005074314 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 433) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/433 `/scratch/stefan/7916156/working/3D/433' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CF)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074314.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074314.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074314/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074314 none CC(CF)C(=O)N1CC(C)(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 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [19, 13, 19, 21, 6, 13, 6, 6, 4, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 6, 19, 19, 19, 19, 21, 21, 6, 6, 6, 6, 6, 5, 1, 6, 6] 21 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: 81 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074314 none CC(CF)C(=O)N1CC(C)(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 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 12, 21, 1, 6, 1, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 6, 1, 12, 12, 12, 12, 21, 21, 1, 1, 2, 2, 2, 3, 6, 1, 1] 21 rigid atoms, others: [33, 34, 4, 6, 7, 8, 9, 10, 19, 26, 27] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074314 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074314 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074314/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074314 Building REAL250005074315 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074315' /scratch/stefan/7916156/working/building/REAL250005074315 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074315 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074315/0 /scratch/stefan/7916156/working/building/REAL250005074315 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 434) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/434 `/scratch/stefan/7916156/working/3D/434' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(Cl)=CC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074315.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074315/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074315 none CC(Cl)=CC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 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', 'C.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, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 15, 8, 15, 8, 8, 6, 8, 6, 1, 6, 1, 1, 1, 1, 1, 1, 8, 27, 27, 27, 27, 8, 8, 8, 8, 8, 7, 1, 8, 8] 27 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32]) total number of confs: 81 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074315 none CC(Cl)=CC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 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', 'C.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, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 5, 1, 5, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 1, 20, 20, 20, 20, 1, 1, 2, 2, 2, 3, 8, 1, 1] 27 rigid atoms, others: [32, 4, 6, 7, 8, 9, 10, 19, 24, 25, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 26, 27, 28, 29, 30]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074315 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074315 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074315/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074315 Building REAL250005074316 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074316' /scratch/stefan/7916156/working/building/REAL250005074316 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074316 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074316/0 /scratch/stefan/7916156/working/building/REAL250005074316 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 435) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/435 `/scratch/stefan/7916156/working/3D/435' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074316.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074316.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074316/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074316 none CC=CC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 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 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 15, 8, 15, 8, 8, 6, 8, 6, 1, 6, 1, 1, 1, 1, 1, 1, 8, 19, 19, 19, 19, 19, 8, 8, 8, 8, 8, 7, 1, 8, 8] 19 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: 59 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074316 none CC=CC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 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 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 5, 1, 5, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 1, 13, 13, 13, 12, 12, 1, 1, 2, 2, 2, 3, 8, 1, 1] 19 rigid atoms, others: [32, 3, 5, 6, 7, 8, 9, 18, 24, 25, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074316 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074316 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074316/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074316 Building REAL250005074317 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074317' /scratch/stefan/7916156/working/building/REAL250005074317 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074317 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074317/0 /scratch/stefan/7916156/working/building/REAL250005074317 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 436) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/436 `/scratch/stefan/7916156/working/3D/436' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C(=O)N2CC(C)(NC(=O)C3=CC(=O)[N-]O3)C2)CC1F) `REAL250005074317.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074317/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074317 none CC1(C(=O)N2CC(C)(NC(=O)C3=CC(=O)[N-]O3)C2)CC1F 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', 'F', '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, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 1, 5, 1, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 8, 1, 9, 9, 9, 9, 9, 9, 1, 1, 2, 2, 2, 2, 8, 1, 1, 9, 9, 9] 14 rigid atoms, others: [32, 2, 4, 5, 6, 7, 8, 17, 24, 25, 31] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 33, 34, 35]) total number of confs: 43 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074317 none CC1(C(=O)N2CC(C)(NC(=O)C3=CC(=O)[N-]O3)C2)CC1F 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', 'F', '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, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 4, 4, 9, 9, 9, 9, 11, 11, 11, 14, 14, 14, 14, 14, 9, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 9, 11, 14, 9, 9, 1, 1, 1] 14 rigid atoms, others: [0, 1, 2, 35, 33, 34, 18, 19, 20] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074317 none CC1(C(=O)N2CC(C)(NC(=O)C3=CC(=O)[N-]O3)C2)CC1F 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', 'F', '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, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [14, 12, 8, 12, 8, 8, 7, 8, 7, 1, 7, 1, 1, 1, 1, 1, 1, 8, 14, 14, 14, 14, 14, 14, 8, 8, 8, 8, 8, 7, 1, 8, 8, 14, 14, 14] 14 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 39 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074317 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074317 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074317/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074317 Building REAL250005074318 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074318' /scratch/stefan/7916156/working/building/REAL250005074318 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074318 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074318/0 /scratch/stefan/7916156/working/building/REAL250005074318 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 437) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/437 `/scratch/stefan/7916156/working/3D/437' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C=CCF)C1) `REAL250005074318.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074318/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074318 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C=CCF)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 1, 5, 15, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 10, 10, 10, 18, 18, 34, 34, 44, 10, 10, 10, 10, 6, 1, 10, 10, 34, 34, 44, 44, 10, 10] 44 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 24] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 159 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074318 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C=CCF)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 1, 5, 15, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 10, 1, 1, 1, 6, 6, 16, 16, 28, 1, 2, 2, 2, 3, 10, 1, 1, 16, 16, 28, 28, 1, 1] 44 rigid atoms, others: [0, 1, 2, 32, 11, 12, 13, 19, 25, 26, 31] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 27, 28, 29, 30]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074318 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074318 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074318/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074318 Building REAL250005074319 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074319' /scratch/stefan/7916156/working/building/REAL250005074319 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074319 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074319/0 /scratch/stefan/7916156/working/building/REAL250005074319 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 438) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/438 `/scratch/stefan/7916156/working/3D/438' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2(CO)CC2)C1) `REAL250005074319.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074319/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074319 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2(CO)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [13, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 13, 13, 13, 30, 30, 45, 51, 45, 45, 13, 13, 13, 13, 8, 1, 13, 13, 51, 51, 153, 45, 45, 45, 45, 13, 13] 153 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 25] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 322 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074319 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2(CO)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 3, 3, 3, 13, 13, 13, 13, 13, 1, 1, 1, 7, 7, 15, 36, 15, 15, 1, 2, 2, 2, 3, 13, 1, 1, 36, 36, 108, 15, 15, 15, 15, 1, 1] 153 rigid atoms, others: [0, 1, 2, 35, 36, 11, 12, 13, 20, 26, 27] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 263 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.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: REAL250005074319 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2(CO)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 15, 26, 26, 26, 45, 45, 45, 45, 45, 15, 5, 1, 5, 1, 1, 10, 1, 1, 15, 15, 15, 15, 26, 45, 15, 15, 10, 10, 30, 1, 1, 1, 1, 15, 15] 153 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, 35, 36]) total number of confs: 157 number of broken/clashed sets: 6 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074319 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074319 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074319/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074319 Building REAL250005074320 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074320' /scratch/stefan/7916156/working/building/REAL250005074320 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074320 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074320/0 /scratch/stefan/7916156/working/building/REAL250005074320 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 439) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/439 `/scratch/stefan/7916156/working/3D/439' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=CC=NO2)C1) `REAL250005074320.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074320/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074320 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=CC=NO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 1, 1, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 11, 11, 11, 21, 21, 31, 31, 31, 31, 11, 11, 11, 11, 7, 1, 11, 11, 31, 31, 11, 11] 31 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 25] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31]) total number of confs: 81 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074320 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=CC=NO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 1, 1, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 3, 3, 3, 11, 11, 11, 11, 11, 1, 1, 1, 6, 6, 16, 16, 16, 16, 1, 2, 2, 2, 3, 11, 1, 1, 17, 16, 1, 1] 31 rigid atoms, others: [0, 1, 2, 11, 12, 13, 20, 26, 27, 30, 31] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074320 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=CC=NO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 1, 1, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 28, 28, 28, 31, 31, 31, 31, 31, 17, 7, 1, 7, 1, 1, 1, 1, 1, 16, 17, 17, 17, 28, 31, 17, 17, 1, 1, 16, 16] 31 rigid atoms, others: [13, 15, 16, 17, 18, 19, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31]) total number of confs: 81 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074320 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074320 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074320/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074320 Building REAL250005074321 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074321' /scratch/stefan/7916156/working/building/REAL250005074321 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types Protomer extracton resulted in 0 protomers Marking REAL250005074321 as failed and skipping /scratch/stefan/7916156/working /scratch/stefan/7916156 `/scratch/stefan/7916156/working/building/REAL250005074321' -> `/scratch/stefan/7916156/failed/REAL250005074321' Building REAL250005074322 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074322' /scratch/stefan/7916156/working/building/REAL250005074322 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074322 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074322/0 /scratch/stefan/7916156/working/building/REAL250005074322 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 440) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/440 `/scratch/stefan/7916156/working/3D/440' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074322.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074322/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074322 none C[C@H](O)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [24, 13, 24, 24, 7, 13, 7, 7, 5, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 24, 24, 24, 72, 7, 7, 7, 7, 7, 6, 1, 6, 6] 72 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32]) total number of confs: 171 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074322 none C[C@H](O)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [13, 4, 13, 13, 1, 4, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 1, 13, 13, 13, 39, 1, 1, 2, 2, 2, 2, 7, 1, 1] 72 rigid atoms, others: [32, 4, 6, 7, 8, 9, 10, 19, 24, 25, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 26, 27, 28, 29, 30]) total number of confs: 98 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074322 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074322 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074322/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074322 Building REAL250005074323 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074323' /scratch/stefan/7916156/working/building/REAL250005074323 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074323 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074323/0 /scratch/stefan/7916156/working/building/REAL250005074323 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 441) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/441 `/scratch/stefan/7916156/working/3D/441' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CON=CC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074323.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074323/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074323 none CON=CC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 19, 9, 19, 9, 9, 8, 9, 8, 1, 8, 1, 1, 1, 1, 1, 1, 9, 37, 37, 37, 37, 9, 9, 9, 9, 9, 8, 1, 9, 9] 37 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32]) total number of confs: 109 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074323 none CON=CC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [30, 27, 27, 6, 1, 6, 1, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 1, 30, 30, 30, 27, 1, 1, 2, 2, 2, 3, 9, 1, 1] 37 rigid atoms, others: [32, 4, 6, 7, 8, 9, 10, 19, 24, 25, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 26, 27, 28, 29, 30]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074323 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074323 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074323/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074323 Building REAL250005074324 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074324' /scratch/stefan/7916156/working/building/REAL250005074324 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074324 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074324/0 /scratch/stefan/7916156/working/building/REAL250005074324 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 442) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/442 `/scratch/stefan/7916156/working/3D/442' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](O)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074324.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074324/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074324 none CC(C)[C@H](O)C(=O)N1CC(C)(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 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [39, 33, 40, 18, 33, 33, 8, 18, 8, 7, 6, 7, 6, 1, 6, 1, 1, 1, 1, 1, 1, 7, 40, 40, 40, 40, 40, 40, 40, 99, 8, 8, 8, 8, 8, 6, 1, 7, 7] 120 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: 274 number of broken/clashed sets: 13 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074324 none CC(C)[C@H](O)C(=O)N1CC(C)(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 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [30, 21, 31, 7, 21, 21, 1, 7, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 1, 31, 31, 31, 31, 31, 31, 31, 63, 1, 1, 2, 2, 2, 2, 7, 1, 1] 120 rigid atoms, others: [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, 32, 33, 34, 35, 36]) total number of confs: 213 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074324 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074324 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074324/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074324 Building REAL250005074325 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074325' /scratch/stefan/7916156/working/building/REAL250005074325 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074325 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074325/0 /scratch/stefan/7916156/working/building/REAL250005074325 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 443) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/443 `/scratch/stefan/7916156/working/3D/443' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CC1(C(=O)N2CC(C)(NC(=O)C3=CC(=O)[N-]O3)C2)CC1) `REAL250005074325.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074325/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074325 none C#CC1(C(=O)N2CC(C)(NC(=O)C3=CC(=O)[N-]O3)C2)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', '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, 5, 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] 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: [14, 14, 6, 1, 6, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 1, 14, 14, 14, 1, 1, 2, 2, 2, 2, 6, 1, 1, 14, 14, 14, 14] 20 rigid atoms, others: [3, 5, 6, 7, 8, 9, 18, 22, 23, 29, 30] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 24, 25, 26, 27, 28, 31, 32, 33, 34]) total number of confs: 55 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074325 none C#CC1(C(=O)N2CC(C)(NC(=O)C3=CC(=O)[N-]O3)C2)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', '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, 5, 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] 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, 5, 5, 14, 14, 14, 14, 18, 18, 18, 20, 20, 20, 20, 20, 14, 1, 1, 1, 14, 14, 14, 14, 14, 18, 20, 14, 14, 1, 1, 1, 1] 20 rigid atoms, others: [0, 1, 2, 3, 33, 32, 34, 19, 20, 21, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074325 none C#CC1(C(=O)N2CC(C)(NC(=O)C3=CC(=O)[N-]O3)C2)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', '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, 5, 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] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 13, 6, 13, 6, 6, 5, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 20, 20, 20, 6, 6, 6, 6, 6, 5, 1, 6, 6, 20, 20, 20, 20] 20 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34]) total number of confs: 61 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074325 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074325 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074325/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074325 Building REAL250005074326 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074326' /scratch/stefan/7916156/working/building/REAL250005074326 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074326 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074326/0 /scratch/stefan/7916156/working/building/REAL250005074326 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 444) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/444 `/scratch/stefan/7916156/working/3D/444' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC=CCC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074326.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074326.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074326/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074326 none C=CC=CCC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 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, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [109, 109, 109, 84, 22, 10, 22, 10, 10, 8, 10, 8, 1, 8, 1, 1, 1, 1, 1, 1, 10, 109, 109, 109, 109, 109, 84, 84, 10, 10, 10, 10, 10, 8, 1, 10, 10] 109 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: 397 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074326 none C=CC=CCC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 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, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [89, 84, 84, 37, 6, 1, 6, 1, 1, 1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 10, 1, 89, 89, 89, 84, 84, 37, 37, 1, 1, 2, 2, 2, 3, 10, 1, 1] 109 rigid atoms, others: [35, 36, 5, 7, 8, 9, 10, 11, 20, 28, 29] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34]) total number of confs: 310 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074326 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074326 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074326/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074326 Building REAL250005074327 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074327' /scratch/stefan/7916156/working/building/REAL250005074327 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074327 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074327/0 /scratch/stefan/7916156/working/building/REAL250005074327 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 445) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/445 `/scratch/stefan/7916156/working/3D/445' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#C[C@H]1C[C@H]1C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074327.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074327.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074327/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074327 none C#C[C@H]1C[C@H]1C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 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', 'C.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, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 5, 13, 1, 5, 1, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 6, 1, 13, 13, 13, 1, 1, 2, 2, 2, 3, 6, 1, 1] 18 rigid atoms, others: [33, 34, 7, 9, 10, 11, 12, 13, 22, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 28, 29, 30, 31, 32]) total number of confs: 49 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074327 none C#C[C@H]1C[C@H]1C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 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', 'C.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, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 13, 13, 13, 13, 17, 17, 17, 18, 18, 18, 18, 18, 13, 1, 1, 1, 13, 13, 13, 13, 13, 17, 18, 13, 13] 18 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 23, 24, 25] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074327 none C#C[C@H]1C[C@H]1C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 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', 'C.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, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 11, 18, 6, 11, 6, 6, 4, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 6, 18, 18, 18, 6, 6, 6, 6, 6, 5, 1, 6, 6] 18 rigid atoms, others: [32, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34]) total number of confs: 57 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074327 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074327 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074327/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074327 Building REAL250005074328 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074328' /scratch/stefan/7916156/working/building/REAL250005074328 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074328 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074328/0 /scratch/stefan/7916156/working/building/REAL250005074328 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 446) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/446 `/scratch/stefan/7916156/working/3D/446' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=C(CC)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074328.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074328.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074328/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074328 none CC=C(CC)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 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', 'C.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, 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 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 16, 27, 38, 8, 16, 8, 8, 6, 8, 6, 1, 6, 1, 1, 1, 1, 1, 1, 8, 27, 27, 27, 27, 38, 38, 38, 38, 38, 8, 8, 8, 8, 8, 6, 1, 8, 8] 38 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: 153 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074328 none CC=C(CC)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 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', 'C.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, 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 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 5, 17, 26, 1, 5, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 1, 17, 17, 17, 17, 26, 26, 26, 26, 26, 1, 1, 2, 2, 2, 3, 8, 1, 1] 38 rigid atoms, others: [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, 32, 33, 34, 35, 36]) total number of confs: 117 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074328 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074328 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074328/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074328 Building REAL250005074329 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074329' /scratch/stefan/7916156/working/building/REAL250005074329 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074329 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074329/0 /scratch/stefan/7916156/working/building/REAL250005074329 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 447) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/447 `/scratch/stefan/7916156/working/3D/447' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(F)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074329.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074329/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074329 none COC(F)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 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', 'C.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, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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, 43, 20, 43, 8, 20, 8, 8, 6, 8, 6, 1, 6, 1, 1, 1, 1, 1, 1, 8, 44, 44, 44, 43, 8, 8, 8, 8, 8, 7, 1, 8, 8] 44 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32]) total number of confs: 159 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074329 none COC(F)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 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', 'C.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, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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: [36, 25, 6, 25, 1, 6, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 1, 36, 36, 36, 25, 1, 1, 2, 2, 2, 3, 8, 1, 1] 44 rigid atoms, others: [32, 4, 6, 7, 8, 9, 10, 19, 24, 25, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 26, 27, 28, 29, 30]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074329 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074329 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074329/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074329 Building REAL250005074330 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074330' /scratch/stefan/7916156/working/building/REAL250005074330 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074330 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074330/0 /scratch/stefan/7916156/working/building/REAL250005074330 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 448) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/448 `/scratch/stefan/7916156/working/3D/448' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(O)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074330.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074330/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074330 none COCC(O)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 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', '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, 12, 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, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 240 conformations in input total number of sets (complete confs): 240 using faster count positions algorithm for large data unique positions, atoms: [80, 80, 59, 20, 59, 9, 20, 9, 9, 7, 9, 7, 1, 7, 1, 1, 1, 1, 1, 1, 9, 80, 80, 80, 80, 80, 59, 177, 9, 9, 9, 9, 9, 8, 1, 9, 9] 240 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: 509 number of broken/clashed sets: 32 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074330 none COCC(O)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 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', '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, 12, 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, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 240 conformations in input total number of sets (complete confs): 240 using faster count positions algorithm for large data unique positions, atoms: [71, 59, 31, 6, 31, 1, 6, 1, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 1, 71, 71, 71, 59, 59, 31, 93, 1, 1, 2, 2, 2, 3, 9, 1, 1] 240 rigid atoms, others: [35, 36, 5, 7, 8, 9, 10, 11, 20, 28, 29] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34]) total number of confs: 374 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074330 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074330 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074330/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074330 Building REAL250005074331 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074331' /scratch/stefan/7916156/working/building/REAL250005074331 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074331 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074331/0 /scratch/stefan/7916156/working/building/REAL250005074331 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 449) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/449 `/scratch/stefan/7916156/working/3D/449' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)[C@@H]2C[C@H]2C#N)C1) `REAL250005074331.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074331/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074331 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)[C@@H]2C[C@H]2C#N)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [13, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 13, 13, 13, 29, 29, 56, 56, 56, 56, 56, 56, 13, 13, 13, 13, 7, 1, 13, 13, 56, 56, 13, 13] 56 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 27] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33]) total number of confs: 175 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074331 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)[C@@H]2C[C@H]2C#N)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 3, 3, 3, 13, 13, 13, 13, 13, 1, 1, 1, 6, 6, 27, 27, 27, 27, 27, 27, 1, 2, 2, 2, 3, 13, 1, 1, 27, 27, 1, 1] 56 rigid atoms, others: [0, 1, 2, 33, 32, 11, 12, 13, 22, 28, 29] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 30, 31]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074331 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)[C@@H]2C[C@H]2C#N)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 45, 45, 45, 56, 56, 56, 56, 56, 27, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 45, 56, 27, 27, 1, 1, 27, 27] 56 rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33]) total number of confs: 138 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074331 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074331 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074331/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074331 Building REAL250005074332 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074332' /scratch/stefan/7916156/working/building/REAL250005074332 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074332 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074332/0 /scratch/stefan/7916156/working/building/REAL250005074332 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 450) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/450 `/scratch/stefan/7916156/working/3D/450' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)[C@H]2C[C@@H](O)C2)C1) `REAL250005074332.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074332/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074332 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)[C@H]2C[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 5, 7, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [13, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 13, 13, 13, 28, 28, 51, 51, 51, 51, 51, 51, 13, 13, 13, 13, 6, 1, 13, 13, 51, 51, 153, 51, 51, 13, 13] 153 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 27] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 314 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074332 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)[C@H]2C[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 5, 7, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 3, 3, 3, 13, 13, 13, 13, 13, 1, 1, 1, 6, 6, 25, 25, 25, 25, 25, 25, 1, 2, 2, 2, 3, 13, 1, 1, 25, 25, 75, 25, 25, 1, 1] 153 rigid atoms, others: [0, 1, 2, 35, 36, 11, 12, 13, 22, 28, 29] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.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: REAL250005074332 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)[C@H]2C[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 5, 7, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 25, 40, 40, 40, 51, 51, 51, 51, 51, 25, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 40, 51, 25, 25, 1, 1, 3, 1, 1, 25, 25] 153 rigid atoms, others: [33, 34, 13, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 22, 23, 24, 25, 26, 27, 28, 29, 32, 35, 36]) total number of confs: 126 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074332 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074332 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074332/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074332 Building REAL250005074333 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074333' /scratch/stefan/7916156/working/building/REAL250005074333 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074333 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074333/0 /scratch/stefan/7916156/working/building/REAL250005074333 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 451) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/451 `/scratch/stefan/7916156/working/3D/451' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)COCCO)C1) `REAL250005074333.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074333/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074333 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)COCCO)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 12, 5, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [8, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 8, 8, 8, 22, 22, 86, 142, 201, 201, 8, 8, 8, 8, 4, 1, 8, 8, 86, 86, 201, 201, 201, 201, 603, 8, 8] 603 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 25] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 1289 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074333 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)COCCO)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 12, 5, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 1, 1, 1, 6, 6, 35, 82, 141, 160, 1, 2, 2, 2, 3, 8, 1, 1, 35, 35, 141, 141, 160, 160, 480, 1, 1] 603 rigid atoms, others: [0, 1, 2, 35, 36, 11, 12, 13, 20, 26, 27] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 1092 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074333 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074333 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074333/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074333 Building REAL250005074334 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074334' /scratch/stefan/7916156/working/building/REAL250005074334 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074334 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074334/0 /scratch/stefan/7916156/working/building/REAL250005074334 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 452) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/452 `/scratch/stefan/7916156/working/3D/452' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(CF)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074334.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074334/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074334 none CC(C)(CF)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 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', '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, 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, 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] 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: [42, 20, 42, 42, 44, 7, 20, 7, 7, 5, 7, 5, 1, 5, 1, 1, 1, 1, 1, 1, 7, 42, 42, 42, 42, 42, 42, 44, 44, 7, 7, 7, 7, 7, 5, 1, 7, 7] 44 rigid atoms, others: [35, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37]) total number of confs: 171 number of broken/clashed sets: 36 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074334 none CC(C)(CF)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 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', '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, 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, 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] 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: [19, 7, 19, 19, 34, 1, 7, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 1, 19, 19, 19, 19, 19, 19, 34, 34, 1, 1, 2, 2, 2, 3, 7, 1, 1] 44 rigid atoms, others: [36, 5, 7, 8, 9, 10, 11, 20, 29, 30, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35]) total number of confs: 173 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074334 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074334 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074334/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074334 Building REAL250005074335 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074335' /scratch/stefan/7916156/working/building/REAL250005074335 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074335 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074335/0 /scratch/stefan/7916156/working/building/REAL250005074335 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 453) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/453 `/scratch/stefan/7916156/working/3D/453' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(CO)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074335.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074335.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074335/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074335 none CC(C)(CO)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 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', 'C.3', 'H', 'H', '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, 5, 7, 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, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [33, 19, 33, 33, 34, 9, 19, 9, 9, 7, 9, 7, 1, 7, 1, 1, 1, 1, 1, 1, 9, 33, 33, 33, 33, 33, 33, 34, 34, 102, 9, 9, 9, 9, 9, 7, 1, 9, 9] 102 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: 229 number of broken/clashed sets: 90 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074335 none CC(C)(CO)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 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', 'C.3', 'H', 'H', '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, 5, 7, 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, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [17, 7, 17, 17, 26, 1, 7, 1, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 1, 17, 17, 17, 17, 17, 17, 26, 26, 78, 1, 1, 2, 2, 2, 3, 9, 1, 1] 102 rigid atoms, others: [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, 32, 33, 34, 35, 36]) total number of confs: 205 number of broken/clashed sets: 90 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074335 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074335 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074335/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074335 Building REAL250005074336 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074336' /scratch/stefan/7916156/working/building/REAL250005074336 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074336 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074336/0 /scratch/stefan/7916156/working/building/REAL250005074336 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 454) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/454 `/scratch/stefan/7916156/working/3D/454' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(C)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074336.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074336/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074336 none C=CCC(C)C(=O)N1CC(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, 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 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [73, 73, 54, 21, 54, 8, 21, 8, 8, 5, 8, 5, 1, 5, 1, 1, 1, 1, 1, 1, 8, 73, 73, 73, 73, 73, 54, 54, 54, 54, 8, 8, 8, 8, 8, 6, 1, 8, 8] 73 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: 306 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074336 none C=CCC(C)C(=O)N1CC(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, 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 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [64, 54, 26, 7, 26, 1, 7, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 1, 64, 64, 64, 54, 54, 26, 26, 26, 26, 1, 1, 2, 2, 2, 3, 8, 1, 1] 73 rigid atoms, others: [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, 32, 33, 34, 35, 36]) total number of confs: 281 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074336 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074336 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074336/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074336 Building REAL250005074337 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074337' /scratch/stefan/7916156/working/building/REAL250005074337 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074337 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074337/0 /scratch/stefan/7916156/working/building/REAL250005074337 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 455) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/455 `/scratch/stefan/7916156/working/3D/455' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H]1C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074337.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074337.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074337/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074337 none C[C@@H]1C[C@H]1C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 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, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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: [20, 20, 20, 20, 6, 20, 1, 6, 1, 1, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 9, 1, 20, 20, 20, 20, 20, 1, 1, 2, 2, 2, 2, 9, 1, 1] 31 rigid atoms, others: [34, 35, 6, 8, 9, 10, 11, 12, 21, 27, 28] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 70 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074337 none C[C@@H]1C[C@H]1C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 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, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 8, 8, 20, 20, 20, 20, 27, 27, 27, 31, 31, 31, 31, 31, 20, 2, 2, 2, 1, 1, 20, 20, 20, 20, 20, 27, 31, 20, 20] 31 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 25, 26] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35]) 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.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: REAL250005074337 none C[C@@H]1C[C@H]1C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 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, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 20, 31, 9, 20, 9, 9, 6, 9, 6, 1, 6, 1, 1, 1, 1, 1, 1, 9, 31, 31, 31, 31, 31, 9, 9, 10, 10, 10, 6, 1, 9, 9] 31 rigid atoms, others: [33, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35]) total number of confs: 103 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074337 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074337 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074337/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074337 Building REAL250005074338 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074338' /scratch/stefan/7916156/working/building/REAL250005074338 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074338 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074338/0 /scratch/stefan/7916156/working/building/REAL250005074338 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 456) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/456 `/scratch/stefan/7916156/working/3D/456' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(O)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074338.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074338/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074338 none CC(C)(O)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [18, 12, 18, 18, 6, 12, 6, 6, 4, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 6, 18, 18, 18, 18, 18, 18, 54, 6, 6, 6, 6, 6, 4, 1, 6, 6] 54 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: 118 number of broken/clashed sets: 18 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074338 none CC(C)(O)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [12, 6, 12, 12, 1, 6, 1, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 6, 1, 12, 12, 12, 12, 12, 12, 36, 1, 1, 2, 2, 2, 3, 6, 1, 1] 54 rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 10, 19, 27, 28] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 95 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074338 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074338 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074338/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074338 Building REAL250005074339 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074339' /scratch/stefan/7916156/working/building/REAL250005074339 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074339 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074339/0 /scratch/stefan/7916156/working/building/REAL250005074339 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 457) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/457 `/scratch/stefan/7916156/working/3D/457' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=NOCC2)C1) `REAL250005074339.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074339/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074339 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=NOCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 8, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 8, 8, 8, 22, 22, 42, 42, 42, 42, 8, 8, 8, 8, 5, 1, 8, 8, 42, 42, 42, 42, 8, 8] 42 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 25] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 99 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074339 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=NOCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 8, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 1, 1, 1, 6, 6, 32, 32, 32, 32, 1, 2, 2, 2, 3, 8, 1, 1, 32, 32, 32, 32, 1, 1] 42 rigid atoms, others: [0, 1, 2, 33, 32, 11, 12, 13, 20, 26, 27] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30, 31]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up 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: REAL250005074339 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=NOCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 8, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 37, 37, 37, 42, 42, 42, 42, 42, 32, 10, 1, 10, 1, 1, 1, 1, 1, 32, 33, 33, 33, 37, 42, 32, 32, 1, 1, 1, 1, 32, 32] 42 rigid atoms, others: [13, 15, 16, 17, 18, 19, 28, 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, 32, 33]) total number of confs: 89 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074339 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074339 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074339/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074339 Building REAL250005074340 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074340' /scratch/stefan/7916156/working/building/REAL250005074340 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074340 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074340/0 /scratch/stefan/7916156/working/building/REAL250005074340 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 458) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/458 `/scratch/stefan/7916156/working/3D/458' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C#N)CC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074340.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074340/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074340 none CC(C#N)CC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [49, 41, 49, 49, 14, 8, 14, 8, 8, 6, 8, 6, 1, 6, 1, 1, 1, 1, 1, 1, 8, 49, 49, 49, 49, 41, 41, 8, 8, 8, 8, 8, 6, 1, 8, 8] 49 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: 193 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074340 none CC(C#N)CC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [38, 25, 38, 37, 5, 1, 5, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 1, 38, 38, 38, 38, 25, 25, 1, 1, 2, 2, 2, 3, 8, 1, 1] 49 rigid atoms, others: [34, 35, 5, 7, 8, 9, 10, 11, 20, 27, 28] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074340 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074340 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074340/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074340 Building REAL250005074341 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074341' /scratch/stefan/7916156/working/building/REAL250005074341 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074341 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074341/0 /scratch/stefan/7916156/working/building/REAL250005074341 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 459) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/459 `/scratch/stefan/7916156/working/3D/459' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCO)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074341.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074341/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074341 none CC(CCO)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 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', 'C.3', 'H', 'H', '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, 5, 7, 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, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [26, 17, 26, 31, 32, 10, 17, 10, 10, 8, 10, 8, 1, 8, 1, 1, 1, 1, 1, 1, 10, 26, 26, 26, 26, 32, 32, 31, 32, 96, 10, 10, 10, 10, 10, 8, 1, 10, 10] 96 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: 219 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074341 none CC(CCO)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 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', 'C.3', 'H', 'H', '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, 5, 7, 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, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [13, 6, 13, 19, 25, 1, 6, 1, 1, 1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 10, 1, 13, 13, 13, 13, 20, 20, 24, 25, 75, 1, 1, 2, 2, 2, 3, 10, 1, 1] 96 rigid atoms, others: [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, 32, 33, 34, 35, 36]) total number of confs: 202 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074341 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074341 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074341/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074341 Building REAL250005074342 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074342' /scratch/stefan/7916156/working/building/REAL250005074342 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074342 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074342/0 /scratch/stefan/7916156/working/building/REAL250005074342 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 460) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/460 `/scratch/stefan/7916156/working/3D/460' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)[C@H](O)CF)C1) `REAL250005074342.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074342/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074342 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)[C@H](O)CF)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 12, 5, 15, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 132 conformations in input total number of sets (complete confs): 132 using faster count positions algorithm for large data unique positions, atoms: [10, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 10, 10, 10, 21, 21, 38, 38, 38, 44, 10, 10, 10, 10, 6, 1, 10, 10, 114, 44, 44, 10, 10] 132 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 25] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 289 number of broken/clashed sets: 14 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074342 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)[C@H](O)CF)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 12, 5, 15, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 132 conformations in input total number of sets (complete confs): 132 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 10, 1, 1, 1, 6, 6, 19, 19, 19, 32, 1, 2, 2, 2, 3, 10, 1, 1, 57, 32, 32, 1, 1] 132 rigid atoms, others: [0, 1, 2, 32, 11, 12, 13, 20, 26, 27, 31] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30]) total number of confs: 211 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074342 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074342 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074342/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074342 Building REAL250005074343 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074343' /scratch/stefan/7916156/working/building/REAL250005074343 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074343 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074343/0 /scratch/stefan/7916156/working/building/REAL250005074343 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 461) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/461 `/scratch/stefan/7916156/working/3D/461' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2(O)CCC2)C1) `REAL250005074343.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074343.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074343/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074343 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2(O)CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 132 conformations in input total number of sets (complete confs): 132 using faster count positions algorithm for large data unique positions, atoms: [13, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 13, 13, 13, 30, 30, 44, 44, 44, 44, 13, 13, 13, 13, 6, 1, 13, 13, 132, 44, 44, 44, 44, 44, 44, 13, 13] 132 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 25] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 269 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074343 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2(O)CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 132 conformations in input total number of sets (complete confs): 132 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 3, 3, 3, 13, 13, 13, 13, 13, 1, 1, 1, 7, 7, 28, 28, 28, 28, 1, 2, 2, 2, 3, 13, 1, 1, 84, 28, 28, 28, 28, 28, 28, 1, 1] 132 rigid atoms, others: [0, 1, 2, 35, 36, 11, 12, 13, 20, 26, 27] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 177 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.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: REAL250005074343 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2(O)CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 132 conformations in input total number of sets (complete confs): 132 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 38, 38, 38, 44, 44, 44, 44, 44, 28, 9, 1, 9, 1, 1, 1, 1, 1, 28, 28, 28, 28, 38, 44, 28, 28, 6, 1, 1, 1, 1, 1, 1, 28, 28] 132 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, 35, 36]) total number of confs: 103 number of broken/clashed sets: 10 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074343 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074343 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074343/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074343 Building REAL250005074344 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074344' /scratch/stefan/7916156/working/building/REAL250005074344 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074344 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074344/0 /scratch/stefan/7916156/working/building/REAL250005074344 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 462) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/462 `/scratch/stefan/7916156/working/3D/462' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C(O)C2CC2)C1) `REAL250005074344.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074344/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074344 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C(O)C2CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 165 conformations in input total number of sets (complete confs): 165 using faster count positions algorithm for large data unique positions, atoms: [9, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 9, 9, 9, 21, 21, 44, 44, 55, 55, 9, 9, 9, 9, 7, 1, 9, 9, 44, 132, 55, 55, 55, 55, 55, 9, 9] 165 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 25] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 335 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074344 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C(O)C2CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 165 conformations in input total number of sets (complete confs): 165 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 1, 1, 1, 6, 6, 25, 25, 34, 34, 1, 2, 2, 2, 3, 9, 1, 1, 25, 75, 34, 34, 34, 34, 34, 1, 1] 165 rigid atoms, others: [0, 1, 2, 35, 36, 11, 12, 13, 20, 26, 27] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 214 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.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: REAL250005074344 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C(O)C2CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 165 conformations in input total number of sets (complete confs): 165 using faster count positions algorithm for large data unique positions, atoms: [34, 34, 34, 52, 52, 52, 55, 55, 55, 55, 55, 34, 17, 8, 17, 1, 8, 1, 1, 1, 34, 34, 34, 34, 52, 55, 34, 34, 8, 24, 1, 1, 1, 1, 1, 34, 34] 165 rigid atoms, others: [32, 33, 34, 15, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36]) total number of confs: 180 number of broken/clashed sets: 9 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074344 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074344 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074344/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074344 Building REAL250005074345 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074345' /scratch/stefan/7916156/working/building/REAL250005074345 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074345 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074345/0 /scratch/stefan/7916156/working/building/REAL250005074345 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 463) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/463 `/scratch/stefan/7916156/working/3D/463' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)CC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074345.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074345/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074345 none C=C(C)CC(=O)N1CC(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, 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 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 22, 8, 22, 8, 8, 6, 8, 6, 1, 6, 1, 1, 1, 1, 1, 1, 8, 48, 48, 48, 48, 48, 48, 48, 8, 8, 8, 8, 8, 6, 1, 8, 8] 48 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: 168 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074345 none C=C(C)CC(=O)N1CC(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, 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 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [36, 29, 36, 6, 1, 6, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 1, 36, 36, 36, 36, 36, 29, 29, 1, 1, 2, 2, 2, 3, 8, 1, 1] 48 rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 10, 19, 27, 28] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074345 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074345 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074345/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074345 Building REAL250005074346 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074346' /scratch/stefan/7916156/working/building/REAL250005074346 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074346 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074346/0 /scratch/stefan/7916156/working/building/REAL250005074346 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 464) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/464 `/scratch/stefan/7916156/working/3D/464' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C#N)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074346.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074346/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074346 none CC(C)(C#N)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 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', 'C.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, 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 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [22, 19, 22, 22, 22, 9, 19, 9, 9, 6, 9, 6, 1, 6, 1, 1, 1, 1, 1, 1, 9, 22, 22, 22, 22, 22, 22, 9, 9, 9, 9, 9, 6, 1, 9, 9] 22 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: 67 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074346 none CC(C)(C#N)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 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', 'C.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, 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 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [13, 7, 13, 13, 13, 1, 7, 1, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 1, 13, 13, 13, 13, 13, 13, 1, 1, 2, 2, 2, 3, 9, 1, 1] 22 rigid atoms, others: [34, 35, 5, 7, 8, 9, 10, 11, 20, 27, 28] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 65 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074346 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074346 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074346/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074346 Building REAL250005074347 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074347' /scratch/stefan/7916156/working/building/REAL250005074347 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074347 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074347/0 /scratch/stefan/7916156/working/building/REAL250005074347 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 465) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/465 `/scratch/stefan/7916156/working/3D/465' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCSCC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074347.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074347/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074347 none CCSCC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 5, 1, 11, 8, 5, 5, 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 130 conformations in input total number of sets (complete confs): 130 using faster count positions algorithm for large data unique positions, atoms: [130, 111, 79, 27, 11, 27, 11, 11, 7, 11, 7, 1, 7, 1, 1, 1, 1, 1, 1, 11, 130, 130, 130, 130, 130, 79, 79, 11, 11, 11, 11, 11, 7, 1, 11, 11] 130 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: 455 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074347 none CCSCC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 5, 1, 11, 8, 5, 5, 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 130 conformations in input total number of sets (complete confs): 130 using faster count positions algorithm for large data unique positions, atoms: [110, 80, 32, 6, 1, 6, 1, 1, 1, 1, 1, 3, 3, 3, 11, 11, 11, 11, 11, 1, 110, 110, 110, 110, 110, 32, 32, 1, 1, 2, 2, 2, 3, 11, 1, 1] 130 rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 10, 19, 27, 28] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 371 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074347 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074347 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074347/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074347 Building REAL250005074348 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074348' /scratch/stefan/7916156/working/building/REAL250005074348 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074348 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074348/0 /scratch/stefan/7916156/working/building/REAL250005074348 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 466) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/466 `/scratch/stefan/7916156/working/3D/466' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)=C(C)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074348.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074348/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074348 none CC(C)=C(C)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 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', 'C.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, 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 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 14, 25, 8, 14, 8, 8, 6, 8, 6, 1, 6, 1, 1, 1, 1, 1, 1, 8, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8, 8, 8, 8, 8, 6, 1, 8, 8] 25 rigid atoms, others: [36, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 75 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074348 none CC(C)=C(C)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 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', 'C.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, 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 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 7, 16, 1, 7, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 2, 2, 2, 3, 8, 1, 1] 25 rigid atoms, others: [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, 32, 33, 34, 35, 36]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074348 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074348 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074348/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074348 Building REAL250005074349 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074349' /scratch/stefan/7916156/working/building/REAL250005074349 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074349 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074349/0 /scratch/stefan/7916156/working/building/REAL250005074349 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 467) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/467 `/scratch/stefan/7916156/working/3D/467' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074349.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074349/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074349 none CNC(=O)CC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 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, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 65, 87, 20, 9, 20, 9, 9, 7, 9, 7, 1, 7, 1, 1, 1, 1, 1, 1, 9, 87, 87, 87, 87, 65, 65, 9, 9, 9, 9, 9, 7, 1, 9, 9] 87 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: 315 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074349 none CNC(=O)CC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 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, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [71, 71, 32, 71, 6, 1, 6, 1, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 1, 71, 71, 71, 71, 32, 32, 1, 1, 2, 2, 2, 3, 9, 1, 1] 87 rigid atoms, others: [34, 35, 5, 7, 8, 9, 10, 11, 20, 27, 28] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 244 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074349 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074349 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074349/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074349 Building REAL250005074350 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074350' /scratch/stefan/7916156/working/building/REAL250005074350 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074350 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074350/0 /scratch/stefan/7916156/working/building/REAL250005074350 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 468) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/468 `/scratch/stefan/7916156/working/3D/468' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2CC(F)C2)C1) `REAL250005074350.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074350.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074350/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074350 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2CC(F)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 15, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [12, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 12, 12, 12, 25, 25, 41, 41, 41, 41, 12, 12, 12, 12, 7, 1, 12, 12, 41, 41, 41, 41, 41, 41, 12, 12] 41 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 25] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 133 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074350 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2CC(F)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 15, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 3, 12, 12, 12, 12, 12, 1, 1, 1, 6, 6, 21, 21, 21, 21, 1, 2, 2, 2, 3, 12, 1, 1, 21, 21, 21, 21, 21, 21, 1, 1] 41 rigid atoms, others: [0, 1, 2, 34, 11, 12, 13, 35, 20, 26, 27] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.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: REAL250005074350 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2CC(F)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 15, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 37, 37, 37, 41, 41, 41, 41, 41, 21, 8, 1, 8, 1, 1, 1, 1, 1, 21, 21, 21, 21, 37, 41, 21, 21, 1, 1, 1, 1, 1, 1, 21, 21] 41 rigid atoms, others: [32, 33, 13, 15, 16, 17, 18, 19, 28, 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, 34, 35]) total number of confs: 109 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074350 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074350 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074350/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074350 Building REAL250005074351 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074351' /scratch/stefan/7916156/working/building/REAL250005074351 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074351 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074351/0 /scratch/stefan/7916156/working/building/REAL250005074351 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 469) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/469 `/scratch/stefan/7916156/working/3D/469' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074351.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074351.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074351/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074351 none C=CCC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 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 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 19, 10, 19, 10, 10, 8, 10, 8, 1, 8, 1, 1, 1, 1, 1, 1, 10, 35, 35, 35, 35, 35, 10, 10, 10, 10, 10, 8, 1, 10, 10] 35 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32]) total number of confs: 120 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074351 none C=CCC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 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 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [23, 19, 6, 1, 6, 1, 1, 1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 10, 1, 23, 23, 23, 19, 19, 1, 1, 2, 2, 2, 3, 10, 1, 1] 35 rigid atoms, others: [32, 3, 5, 6, 7, 8, 9, 18, 24, 25, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074351 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074351 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074351/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074351 Building REAL250005074352 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074352' /scratch/stefan/7916156/working/building/REAL250005074352 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005074352 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074352/0 /scratch/stefan/7916156/working/building/REAL250005074352 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 470) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/470 `/scratch/stefan/7916156/working/3D/470' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)CC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074352.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074352/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074352 none C[NH+](C)CC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 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, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [14, 12, 14, 14, 11, 7, 11, 7, 7, 5, 7, 5, 1, 5, 1, 1, 1, 1, 1, 1, 7, 14, 14, 14, 14, 14, 14, 12, 12, 7, 7, 7, 7, 7, 5, 1, 7, 7] 14 rigid atoms, others: [35, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37]) total number of confs: 49 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074352 none C[NH+](C)CC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 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, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 12, 12, 4, 1, 4, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 1, 12, 12, 12, 12, 12, 12, 10, 10, 1, 1, 2, 2, 2, 3, 7, 1, 1] 14 rigid atoms, others: [36, 5, 7, 8, 9, 10, 11, 20, 29, 30, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074352 /scratch/stefan/7916156/working /scratch/stefan/7916156 mkdir: created directory `1' /scratch/stefan/7916156/working/building/REAL250005074352/1 /scratch/stefan/7916156/working/building/REAL250005074352 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 1 (index: 471) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/471 `/scratch/stefan/7916156/working/3D/471' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074352.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005074352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074352/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074352 none CN(C)CC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [31, 29, 31, 16, 7, 16, 7, 7, 5, 7, 5, 1, 5, 1, 1, 1, 1, 1, 1, 7, 31, 31, 31, 31, 31, 31, 29, 29, 7, 7, 7, 7, 7, 5, 1, 7, 7] 31 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]) total number of confs: 102 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074352 none CN(C)CC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [27, 21, 27, 6, 1, 6, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 1, 27, 27, 27, 27, 27, 27, 21, 21, 1, 1, 2, 2, 2, 3, 7, 1, 1] 31 rigid atoms, others: [35, 4, 6, 7, 8, 9, 10, 19, 36, 28, 29] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074352 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074352 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 1: /scratch/stefan/7916156/working/building/REAL250005074352/1.* 0: /scratch/stefan/7916156/working/building/REAL250005074352/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074352 Building REAL250005074353 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074353' /scratch/stefan/7916156/working/building/REAL250005074353 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074353 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074353/0 /scratch/stefan/7916156/working/building/REAL250005074353 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 472) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/472 `/scratch/stefan/7916156/working/3D/472' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)CC#N)C1) `REAL250005074353.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074353/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074353 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)CC#N)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 1, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 9, 9, 9, 16, 16, 32, 32, 9, 9, 9, 9, 5, 1, 9, 9, 32, 32, 9, 9] 32 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 23] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29]) total number of confs: 119 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074353 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)CC#N)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 1, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 1, 1, 1, 4, 4, 20, 20, 1, 2, 2, 2, 3, 9, 1, 1, 20, 20, 1, 1] 32 rigid atoms, others: [0, 1, 2, 11, 12, 13, 18, 24, 25, 28, 29] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 19, 20, 21, 22, 23, 26, 27]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074353 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074353 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074353/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074353 Building REAL250005074354 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074354' /scratch/stefan/7916156/working/building/REAL250005074354 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074354 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074354/0 /scratch/stefan/7916156/working/building/REAL250005074354 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 473) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/473 `/scratch/stefan/7916156/working/3D/473' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2CC2F)C1) `REAL250005074354.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074354/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074354 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2CC2F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 15, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [17, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 17, 17, 17, 35, 35, 49, 49, 49, 17, 17, 17, 17, 9, 1, 17, 17, 49, 49, 49, 49, 17, 17] 49 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 24] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 157 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074354 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2CC2F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 15, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 3, 3, 3, 17, 17, 17, 17, 17, 1, 1, 1, 6, 6, 25, 25, 25, 1, 2, 2, 2, 3, 17, 1, 1, 25, 25, 25, 25, 1, 1] 49 rigid atoms, others: [0, 1, 2, 32, 11, 12, 13, 19, 25, 26, 31] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 27, 28, 29, 30]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074354 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2CC2F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 15, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 40, 40, 40, 49, 49, 49, 49, 49, 25, 9, 1, 9, 1, 1, 1, 1, 25, 25, 25, 25, 40, 49, 25, 25, 1, 1, 1, 1, 25, 25] 49 rigid atoms, others: [13, 15, 16, 17, 18, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32]) total number of confs: 119 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074354 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074354 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074354/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074354 Building REAL250005074355 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074355' /scratch/stefan/7916156/working/building/REAL250005074355 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005074355 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074355/0 /scratch/stefan/7916156/working/building/REAL250005074355 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 474) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/474 `/scratch/stefan/7916156/working/3D/474' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1)[NH+](C)C) `REAL250005074355.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074355/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074355 none C[C@@H](C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1)[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', '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, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 2, 3, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 1, 1, 2, 2, 3, 3, 3, 3, 3, 3] 3 rigid atoms, others: [32, 7, 9, 10, 11, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 9 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074355 none C[C@@H](C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1)[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', '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, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 1, 3, 3, 3, 3, 3, 3, 3, 1, 1, 2, 2, 2, 2, 2, 1, 1, 3, 3, 3, 3, 3, 3] 3 rigid atoms, others: [33, 34, 3, 5, 6, 7, 8, 9, 18, 26, 27] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40]) total number of confs: 17 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074355 /scratch/stefan/7916156/working /scratch/stefan/7916156 mkdir: created directory `1' /scratch/stefan/7916156/working/building/REAL250005074355/1 /scratch/stefan/7916156/working/building/REAL250005074355 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 1 (index: 475) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/475 `/scratch/stefan/7916156/working/3D/475' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1)N(C)C) `REAL250005074355.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005074355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074355/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074355 none C[C@@H](C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', '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, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 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 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [14, 10, 14, 4, 10, 4, 4, 2, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 14, 15, 15, 14, 14, 14, 4, 4, 4, 4, 4, 3, 1, 4, 3, 15, 15, 15, 15, 15, 15] 15 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 62 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074355 none C[C@@H](C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', '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, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 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 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [12, 7, 12, 1, 7, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 3, 1, 12, 13, 13, 12, 12, 12, 1, 1, 2, 2, 2, 2, 4, 1, 1, 13, 13, 13, 13, 13, 13] 15 rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 18, 25, 26] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39]) total number of confs: 57 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074355 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074355 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 1: /scratch/stefan/7916156/working/building/REAL250005074355/1.* 0: /scratch/stefan/7916156/working/building/REAL250005074355/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074355 Building REAL250005074356 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074356' /scratch/stefan/7916156/working/building/REAL250005074356 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074356 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074356/0 /scratch/stefan/7916156/working/building/REAL250005074356 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 476) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/476 `/scratch/stefan/7916156/working/3D/476' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)CCF)C1) `REAL250005074356.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074356/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074356 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)CCF)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 15, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 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: [13, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 13, 13, 13, 31, 31, 55, 59, 13, 13, 13, 13, 6, 1, 13, 13, 55, 55, 59, 59, 13, 13] 59 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 23] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 216 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074356 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)CCF)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 15, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 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: [1, 1, 1, 3, 3, 3, 13, 13, 13, 13, 13, 1, 1, 1, 6, 6, 25, 35, 1, 2, 2, 2, 3, 13, 1, 1, 25, 25, 35, 35, 1, 1] 59 rigid atoms, others: [0, 1, 2, 11, 12, 13, 18, 24, 25, 30, 31] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 19, 20, 21, 22, 23, 26, 27, 28, 29]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074356 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074356 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074356/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074356 Building REAL250005074357 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074357' /scratch/stefan/7916156/working/building/REAL250005074357 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074357 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074357/0 /scratch/stefan/7916156/working/building/REAL250005074357 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 477) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/477 `/scratch/stefan/7916156/working/3D/477' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2C=CCC2)C1) `REAL250005074357.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074357/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074357 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2C=CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 1, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 12, 12, 12, 23, 23, 40, 40, 40, 40, 12, 12, 12, 12, 6, 1, 12, 12, 40, 40, 40, 40, 40, 40, 40, 12, 12] 40 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 25] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 119 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074357 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2C=CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 1, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 3, 3, 3, 12, 12, 12, 12, 12, 1, 1, 1, 6, 6, 25, 25, 25, 25, 1, 2, 2, 2, 3, 12, 1, 1, 25, 25, 25, 25, 25, 25, 25, 1, 1] 40 rigid atoms, others: [0, 1, 2, 35, 36, 11, 12, 13, 20, 26, 27] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 86 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.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: REAL250005074357 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2C=CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 1, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 34, 34, 34, 40, 40, 40, 40, 40, 25, 7, 1, 7, 1, 1, 1, 1, 1, 25, 25, 25, 25, 34, 40, 25, 25, 1, 1, 1, 1, 1, 1, 1, 25, 25] 40 rigid atoms, others: [32, 33, 34, 13, 15, 16, 17, 18, 19, 28, 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, 35, 36]) total number of confs: 87 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074357 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074357 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074357/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074357 Building REAL250005074358 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074358' /scratch/stefan/7916156/working/building/REAL250005074358 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074358 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074358/0 /scratch/stefan/7916156/working/building/REAL250005074358 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 478) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/478 `/scratch/stefan/7916156/working/3D/478' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CC(C)(C)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074358.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074358/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074358 none C#CC(C)(C)C(=O)N1CC(C)(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 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 20, 22, 22, 8, 20, 8, 8, 6, 8, 6, 1, 6, 1, 1, 1, 1, 1, 1, 8, 22, 22, 22, 22, 22, 22, 22, 8, 8, 8, 8, 8, 6, 1, 8, 8] 22 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: 61 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074358 none C#CC(C)(C)C(=O)N1CC(C)(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 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 7, 15, 15, 1, 7, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 1, 15, 15, 15, 15, 15, 15, 15, 1, 1, 2, 2, 2, 3, 8, 1, 1] 22 rigid atoms, others: [35, 36, 5, 7, 8, 9, 10, 11, 20, 28, 29] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34]) total number of confs: 75 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074358 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074358 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074358/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074358 Building REAL250005074359 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074359' /scratch/stefan/7916156/working/building/REAL250005074359 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074359 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074359/0 /scratch/stefan/7916156/working/building/REAL250005074359 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 479) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/479 `/scratch/stefan/7916156/working/3D/479' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](C)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074359.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074359/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074359 none CO[C@H](C)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 1, 11, 8, 5, 5, 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, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [29, 27, 16, 27, 27, 8, 16, 8, 8, 6, 7, 6, 1, 6, 1, 1, 1, 1, 1, 1, 7, 29, 29, 29, 27, 27, 27, 8, 8, 8, 8, 8, 7, 1, 7, 7] 29 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: 111 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074359 none CO[C@H](C)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 1, 11, 8, 5, 5, 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, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [24, 19, 6, 19, 19, 1, 6, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 1, 24, 24, 24, 19, 19, 19, 1, 1, 2, 2, 2, 2, 8, 1, 1] 29 rigid atoms, others: [34, 35, 5, 7, 8, 9, 10, 11, 20, 27, 28] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074359 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074359 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074359/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074359 Building REAL250005074360 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074360' /scratch/stefan/7916156/working/building/REAL250005074360 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074360 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074360/0 /scratch/stefan/7916156/working/building/REAL250005074360 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 480) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/480 `/scratch/stefan/7916156/working/3D/480' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)CCC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074360.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074360/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074360 none CC(=O)CCC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 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', '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, 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, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 88, 116, 67, 21, 10, 21, 10, 10, 7, 10, 7, 1, 7, 1, 1, 1, 1, 1, 1, 10, 116, 116, 116, 88, 88, 67, 67, 10, 10, 10, 10, 10, 7, 1, 10, 10] 116 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: 460 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074360 none CC(=O)CCC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 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', '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, 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, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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: [102, 60, 102, 37, 6, 1, 6, 1, 1, 1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 10, 1, 102, 102, 102, 60, 60, 37, 37, 1, 1, 2, 2, 2, 3, 10, 1, 1] 116 rigid atoms, others: [35, 36, 5, 7, 8, 9, 10, 11, 20, 28, 29] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34]) total number of confs: 401 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074360 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074360 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074360/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074360 Building REAL250005074361 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074361' /scratch/stefan/7916156/working/building/REAL250005074361 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074361 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074361/0 /scratch/stefan/7916156/working/building/REAL250005074361 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 481) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/481 `/scratch/stefan/7916156/working/3D/481' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074361.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074361.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074361/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074361 none C[C@@H](O)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 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 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [16, 9, 16, 16, 6, 9, 6, 6, 4, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 16, 16, 16, 48, 6, 6, 6, 6, 6, 5, 1, 5, 5] 48 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32]) total number of confs: 114 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074361 none C[C@@H](O)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 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 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [9, 3, 9, 9, 1, 3, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 1, 9, 9, 9, 27, 1, 1, 2, 2, 2, 2, 6, 1, 1] 48 rigid atoms, others: [32, 4, 6, 7, 8, 9, 10, 19, 24, 25, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 26, 27, 28, 29, 30]) total number of confs: 74 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074361 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074361 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074361/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074361 Building REAL250005074362 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074362' /scratch/stefan/7916156/working/building/REAL250005074362 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005074362 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074362/0 /scratch/stefan/7916156/working/building/REAL250005074362 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 482) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/482 `/scratch/stefan/7916156/working/3D/482' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)CN2CCC2)C1) `REAL250005074362.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074362/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074362 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)CN2CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [12, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 12, 12, 12, 26, 26, 47, 51, 51, 51, 12, 12, 12, 12, 7, 1, 12, 12, 47, 47, 51, 51, 51, 51, 51, 51, 12, 12] 51 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 25] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 184 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074362 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)CN2CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 3, 3, 3, 12, 12, 12, 12, 12, 1, 1, 1, 6, 6, 26, 34, 34, 34, 1, 2, 2, 2, 3, 12, 1, 1, 26, 26, 34, 34, 34, 34, 34, 34, 1, 1] 51 rigid atoms, others: [0, 1, 2, 36, 37, 11, 12, 13, 20, 26, 27] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up 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: REAL250005074362 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)CN2CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [34, 34, 34, 45, 45, 45, 51, 51, 51, 51, 51, 34, 20, 6, 20, 1, 1, 1, 1, 1, 34, 34, 34, 34, 45, 51, 34, 34, 6, 6, 1, 1, 1, 1, 1, 1, 34, 34] 51 rigid atoms, others: [32, 33, 34, 35, 15, 16, 17, 18, 19, 30, 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, 36, 37]) total number of confs: 134 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074362 /scratch/stefan/7916156/working /scratch/stefan/7916156 mkdir: created directory `1' /scratch/stefan/7916156/working/building/REAL250005074362/1 /scratch/stefan/7916156/working/building/REAL250005074362 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 1 (index: 483) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/483 `/scratch/stefan/7916156/working/3D/483' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C[NH+]2CCC2)C1) `REAL250005074362.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005074362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074362/1/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074362 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C[NH+]2CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 13, 16, 16, 16, 16, 5, 5, 5, 5, 4, 1, 5, 5, 13, 13, 16, 16, 16, 16, 16, 16, 5, 5] 16 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 26] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 61 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074362 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C[NH+]2CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 5, 1, 1, 1, 3, 3, 10, 14, 14, 14, 14, 1, 2, 2, 2, 3, 5, 1, 1, 10, 10, 14, 14, 14, 14, 14, 14, 1, 1] 16 rigid atoms, others: [0, 1, 2, 37, 38, 11, 12, 13, 21, 27, 28] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074362 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C[NH+]2CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 16, 16, 16, 16, 16, 16, 16, 16, 14, 11, 5, 11, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 16, 16, 14, 14, 5, 5, 1, 1, 1, 1, 1, 1, 14, 14] 16 rigid atoms, others: [32, 33, 34, 35, 36, 15, 16, 17, 18, 19, 20, 31] 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, 37, 38]) total number of confs: 49 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074362 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074362 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 1: /scratch/stefan/7916156/working/building/REAL250005074362/1.* 0: /scratch/stefan/7916156/working/building/REAL250005074362/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074362 Building REAL250005074363 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074363' /scratch/stefan/7916156/working/building/REAL250005074363 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074363 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074363/0 /scratch/stefan/7916156/working/building/REAL250005074363 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 484) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/484 `/scratch/stefan/7916156/working/3D/484' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)C(C)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074363.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074363.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074363/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074363 none CC(O)C(C)C(=O)N1CC(C)(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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [14, 10, 14, 5, 10, 3, 5, 3, 3, 2, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 14, 14, 14, 14, 42, 10, 10, 10, 10, 3, 3, 3, 3, 3, 3, 1, 3, 3] 42 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: 104 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074363 none CC(O)C(C)C(=O)N1CC(C)(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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [14, 9, 14, 3, 9, 1, 3, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 3, 1, 14, 14, 14, 14, 42, 9, 9, 9, 9, 1, 1, 2, 2, 2, 2, 3, 1, 1] 42 rigid atoms, others: [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, 32, 33, 34, 35, 36]) total number of confs: 112 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074363 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074363 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074363/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074363 Building REAL250005074364 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074364' /scratch/stefan/7916156/working/building/REAL250005074364 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074364 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074364/0 /scratch/stefan/7916156/working/building/REAL250005074364 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 485) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/485 `/scratch/stefan/7916156/working/3D/485' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C1CC1C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074364.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074364/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074364 none C=C1CC1C(=O)N1CC(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'] 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, 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] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 5, 1, 5, 1, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 8, 1, 20, 20, 20, 20, 20, 1, 1, 2, 2, 2, 2, 9, 1, 1] 30 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 19, 25, 26] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31]) total number of confs: 70 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074364 none C=C1CC1C(=O)N1CC(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'] 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, 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] 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, 10, 10, 20, 20, 20, 20, 26, 26, 26, 30, 30, 30, 30, 30, 20, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 26, 30, 20, 20] 30 rigid atoms, others: [0, 1, 2, 3, 4, 20, 21, 22, 23, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074364 none C=C1CC1C(=O)N1CC(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'] 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, 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] 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, 15, 9, 15, 9, 9, 7, 8, 7, 1, 7, 1, 1, 1, 1, 1, 1, 8, 30, 30, 30, 30, 30, 9, 9, 9, 9, 9, 8, 1, 8, 8] 30 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33]) total number of confs: 95 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074364 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074364 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074364/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074364 Building REAL250005074365 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074365' /scratch/stefan/7916156/working/building/REAL250005074365 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074365 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074365/0 /scratch/stefan/7916156/working/building/REAL250005074365 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 486) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/486 `/scratch/stefan/7916156/working/3D/486' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(OC)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074365.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074365/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074365 none COC(OC)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 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', '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, 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, 3, 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 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [71, 51, 21, 51, 70, 8, 21, 8, 8, 6, 8, 6, 1, 6, 1, 1, 1, 1, 1, 1, 8, 71, 71, 71, 51, 70, 70, 70, 8, 8, 8, 8, 8, 6, 1, 8, 8] 71 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: 252 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074365 none COC(OC)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 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', '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, 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, 3, 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 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [55, 30, 6, 30, 57, 1, 6, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 1, 55, 55, 55, 30, 57, 57, 57, 1, 1, 2, 2, 2, 3, 8, 1, 1] 71 rigid atoms, others: [35, 36, 5, 7, 8, 9, 10, 11, 20, 28, 29] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34]) total number of confs: 206 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074365 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074365 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074365/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074365 Building REAL250005074366 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074366' /scratch/stefan/7916156/working/building/REAL250005074366 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074366 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074366/0 /scratch/stefan/7916156/working/building/REAL250005074366 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 487) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/487 `/scratch/stefan/7916156/working/3D/487' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2(C)COC2)C1) `REAL250005074366.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074366/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074366 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2(C)COC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 9, 9, 9, 17, 17, 21, 21, 21, 21, 9, 9, 9, 9, 4, 1, 9, 9, 21, 21, 21, 21, 21, 21, 21, 9, 9] 21 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 25] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 67 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074366 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2(C)COC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 1, 1, 1, 6, 6, 12, 12, 12, 12, 1, 2, 2, 2, 3, 9, 1, 1, 12, 12, 12, 12, 12, 12, 12, 1, 1] 21 rigid atoms, others: [0, 1, 2, 35, 36, 11, 12, 13, 20, 26, 27] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074366 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2(C)COC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 12, 12, 19, 19, 19, 21, 21, 21, 21, 21, 12, 4, 1, 4, 1, 1, 1, 1, 1, 12, 12, 12, 12, 19, 21, 12, 12, 2, 2, 2, 1, 1, 1, 1, 12, 12] 21 rigid atoms, others: [32, 33, 34, 13, 15, 16, 17, 18, 19, 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, 30, 35, 36]) total number of confs: 58 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074366 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074366 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074366/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074366 Building REAL250005074367 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074367' /scratch/stefan/7916156/working/building/REAL250005074367 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074367 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074367/0 /scratch/stefan/7916156/working/building/REAL250005074367 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 488) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/488 `/scratch/stefan/7916156/working/3D/488' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2CC(=O)N2)C1) `REAL250005074367.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074367/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074367 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2CC(=O)N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 14, 14, 14, 30, 30, 50, 50, 50, 50, 14, 14, 14, 14, 7, 1, 14, 14, 50, 50, 50, 50, 14, 14] 50 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 25] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 147 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074367 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2CC(=O)N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 6, 4, 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: [1, 1, 1, 3, 3, 3, 14, 14, 14, 14, 14, 1, 1, 1, 6, 6, 26, 26, 26, 26, 1, 2, 2, 2, 3, 14, 1, 1, 26, 26, 26, 26, 1, 1] 50 rigid atoms, others: [0, 1, 2, 33, 32, 11, 12, 13, 20, 26, 27] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30, 31]) total number of confs: 90 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.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: REAL250005074367 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2CC(=O)N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 6, 4, 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: [26, 26, 26, 42, 42, 42, 50, 50, 50, 50, 50, 26, 9, 1, 9, 1, 1, 1, 1, 1, 26, 26, 26, 26, 42, 50, 26, 26, 1, 1, 1, 1, 26, 26] 50 rigid atoms, others: [13, 15, 16, 17, 18, 19, 28, 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, 32, 33]) total number of confs: 123 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074367 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074367 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074367/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074367 Building REAL250005074368 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074368' /scratch/stefan/7916156/working/building/REAL250005074368 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074368 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074368/0 /scratch/stefan/7916156/working/building/REAL250005074368 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 489) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/489 `/scratch/stefan/7916156/working/3D/489' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)[C@@H]2CC(=O)N2)C1) `REAL250005074368.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074368.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074368/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074368 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)[C@@H]2CC(=O)N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 6, 4, 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: [13, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 13, 13, 13, 27, 27, 50, 50, 50, 50, 50, 13, 13, 13, 13, 7, 1, 13, 13, 50, 50, 50, 13, 13] 50 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 26] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 153 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074368 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)[C@@H]2CC(=O)N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 6, 4, 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: [1, 1, 1, 3, 3, 3, 13, 13, 13, 13, 13, 1, 1, 1, 6, 6, 27, 27, 27, 27, 27, 1, 2, 2, 2, 3, 13, 1, 1, 27, 27, 27, 1, 1] 50 rigid atoms, others: [0, 1, 2, 33, 32, 11, 12, 13, 21, 27, 28] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 29, 30, 31]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up 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: REAL250005074368 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)[C@@H]2CC(=O)N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 6, 4, 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: [27, 27, 27, 43, 43, 43, 50, 50, 50, 50, 50, 27, 9, 1, 9, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 43, 50, 27, 27, 1, 1, 1, 27, 27] 50 rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 29, 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, 32, 33]) total number of confs: 123 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074368 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074368 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074368/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074368 Building REAL250005074369 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074369' /scratch/stefan/7916156/working/building/REAL250005074369 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074369 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074369/0 /scratch/stefan/7916156/working/building/REAL250005074369 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 490) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/490 `/scratch/stefan/7916156/working/3D/490' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@H](O)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074369.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074369/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074369 none CCC[C@H](O)C(=O)N1CC(C)(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 255 conformations in input total number of sets (complete confs): 255 using faster count positions algorithm for large data unique positions, atoms: [85, 80, 58, 23, 58, 58, 11, 23, 11, 11, 7, 10, 7, 1, 7, 1, 1, 1, 1, 1, 1, 10, 85, 85, 85, 85, 84, 81, 81, 174, 11, 11, 11, 11, 11, 8, 1, 10, 10] 255 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: 552 number of broken/clashed sets: 34 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074369 none CCC[C@H](O)C(=O)N1CC(C)(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 255 conformations in input total number of sets (complete confs): 255 using faster count positions algorithm for large data unique positions, atoms: [65, 56, 30, 6, 30, 30, 1, 6, 1, 1, 1, 1, 1, 2, 2, 2, 10, 10, 10, 10, 10, 1, 65, 65, 65, 65, 64, 57, 57, 90, 1, 1, 2, 2, 2, 2, 11, 1, 1] 255 rigid atoms, others: [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, 32, 33, 34, 35, 36]) total number of confs: 404 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074369 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074369 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074369/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074369 Building REAL250005074370 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074370' /scratch/stefan/7916156/working/building/REAL250005074370 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074370 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074370/0 /scratch/stefan/7916156/working/building/REAL250005074370 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 491) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/491 `/scratch/stefan/7916156/working/3D/491' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2(F)CCC2)C1) `REAL250005074370.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074370.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074370/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074370 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2(F)CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 13, 13, 13, 25, 25, 41, 41, 41, 41, 13, 13, 13, 13, 6, 1, 13, 13, 41, 41, 41, 41, 41, 41, 13, 13] 41 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 25] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 131 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074370 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2(F)CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 3, 13, 13, 13, 13, 13, 1, 1, 1, 6, 6, 27, 27, 27, 27, 1, 2, 2, 2, 3, 13, 1, 1, 27, 27, 27, 27, 27, 27, 1, 1] 41 rigid atoms, others: [0, 1, 2, 34, 11, 12, 13, 35, 20, 26, 27] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074370 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2(F)CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 36, 36, 36, 41, 41, 41, 41, 41, 27, 8, 1, 8, 1, 1, 1, 1, 1, 27, 27, 27, 27, 36, 41, 27, 27, 1, 1, 1, 1, 1, 1, 27, 27] 41 rigid atoms, others: [32, 33, 13, 15, 16, 17, 18, 19, 28, 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, 34, 35]) total number of confs: 89 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074370 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074370 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074370/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074370 Building REAL250005074371 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074371' /scratch/stefan/7916156/working/building/REAL250005074371 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005074371 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074371/0 /scratch/stefan/7916156/working/building/REAL250005074371 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 492) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/492 `/scratch/stefan/7916156/working/3D/492' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=CNC=N2)C1) `REAL250005074371.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074371.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074371/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074371 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=CNC=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 1, 8, 1, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 11, 11, 11, 25, 25, 36, 36, 36, 36, 11, 11, 11, 11, 7, 1, 11, 11, 36, 36, 36, 11, 11] 36 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 25] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 97 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074371 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=CNC=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 1, 8, 1, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 3, 3, 3, 11, 11, 11, 11, 11, 1, 1, 1, 6, 6, 19, 19, 19, 19, 1, 2, 2, 2, 3, 11, 1, 1, 19, 19, 19, 1, 1] 36 rigid atoms, others: [0, 1, 2, 32, 11, 12, 13, 20, 26, 27, 31] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up 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: REAL250005074371 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=CNC=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 1, 8, 1, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 32, 32, 32, 36, 36, 36, 36, 36, 20, 8, 1, 8, 1, 1, 1, 1, 1, 19, 20, 20, 20, 32, 36, 20, 20, 1, 1, 1, 19, 19] 36 rigid atoms, others: [13, 15, 16, 17, 18, 19, 28, 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, 31, 32]) total number of confs: 92 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074371 /scratch/stefan/7916156/working /scratch/stefan/7916156 mkdir: created directory `1' /scratch/stefan/7916156/working/building/REAL250005074371/1 /scratch/stefan/7916156/working/building/REAL250005074371 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 1 (index: 493) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/493 `/scratch/stefan/7916156/working/3D/493' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=CN=CN2)C1) `REAL250005074371.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005074371.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074371/1/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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074371 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=CN=CN2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 1, 8, 1, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [14, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 14, 14, 14, 35, 35, 55, 55, 55, 55, 14, 14, 14, 14, 8, 1, 14, 14, 55, 55, 55, 14, 14] 55 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 25] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 137 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074371 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=CN=CN2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 1, 8, 1, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 3, 3, 3, 14, 14, 14, 14, 14, 1, 1, 1, 6, 6, 31, 31, 31, 31, 1, 2, 2, 2, 3, 14, 1, 1, 31, 31, 31, 1, 1] 55 rigid atoms, others: [0, 1, 2, 32, 11, 12, 13, 20, 26, 27, 31] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30]) total number of confs: 69 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.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: REAL250005074371 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2=CN=CN2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 1, 1, 8, 1, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 31, 46, 46, 46, 55, 55, 55, 55, 55, 31, 12, 1, 12, 1, 1, 1, 1, 1, 31, 31, 31, 31, 46, 55, 31, 31, 1, 1, 1, 31, 31] 55 rigid atoms, others: [13, 15, 16, 17, 18, 19, 28, 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, 31, 32]) total number of confs: 132 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074371 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074371 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 1: /scratch/stefan/7916156/working/building/REAL250005074371/1.* 0: /scratch/stefan/7916156/working/building/REAL250005074371/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074371 Building REAL250005074372 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074372' /scratch/stefan/7916156/working/building/REAL250005074372 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074372 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074372/0 /scratch/stefan/7916156/working/building/REAL250005074372 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 494) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/494 `/scratch/stefan/7916156/working/3D/494' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2CC(=O)C2)C1) `REAL250005074372.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074372/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074372 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2CC(=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 1, 11, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [12, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 12, 12, 12, 21, 21, 35, 35, 35, 35, 12, 12, 12, 12, 8, 1, 12, 12, 35, 35, 35, 35, 35, 12, 12] 35 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 25] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 111 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074372 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2CC(=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 1, 11, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 3, 3, 3, 12, 12, 12, 12, 12, 1, 1, 1, 6, 6, 20, 20, 20, 20, 1, 2, 2, 2, 3, 12, 1, 1, 20, 20, 20, 20, 20, 1, 1] 35 rigid atoms, others: [0, 1, 2, 34, 33, 11, 12, 13, 20, 26, 27] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32]) 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.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: REAL250005074372 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2CC(=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 1, 11, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 30, 30, 30, 35, 35, 35, 35, 35, 20, 7, 1, 7, 1, 1, 1, 1, 1, 20, 20, 20, 20, 30, 35, 20, 20, 1, 1, 1, 1, 1, 20, 20] 35 rigid atoms, others: [32, 13, 15, 16, 17, 18, 19, 28, 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, 33, 34]) total number of confs: 82 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074372 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074372 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074372/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074372 Building REAL250005074373 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074373' /scratch/stefan/7916156/working/building/REAL250005074373 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074373 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074373/0 /scratch/stefan/7916156/working/building/REAL250005074373 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 495) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/495 `/scratch/stefan/7916156/working/3D/495' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2(O)COC2)C1) `REAL250005074373.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074373/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074373 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2(O)COC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 12, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 126 conformations in input total number of sets (complete confs): 126 using faster count positions algorithm for large data unique positions, atoms: [12, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 12, 12, 12, 29, 29, 42, 42, 42, 42, 12, 12, 12, 12, 6, 1, 12, 12, 126, 42, 42, 42, 42, 12, 12] 126 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 25] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 255 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074373 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2(O)COC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 12, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 126 conformations in input total number of sets (complete confs): 126 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 3, 3, 3, 12, 12, 12, 12, 12, 1, 1, 1, 6, 6, 23, 23, 23, 23, 1, 2, 2, 2, 3, 12, 1, 1, 69, 23, 23, 23, 23, 1, 1] 126 rigid atoms, others: [0, 1, 2, 34, 33, 11, 12, 13, 20, 26, 27] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32]) total number of confs: 151 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.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: REAL250005074373 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2(O)COC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 12, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 126 conformations in input total number of sets (complete confs): 126 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 23, 38, 38, 38, 42, 42, 42, 42, 42, 23, 9, 1, 9, 1, 1, 1, 1, 1, 23, 23, 23, 23, 38, 42, 23, 23, 3, 1, 1, 1, 1, 23, 23] 126 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, 33, 34]) total number of confs: 110 number of broken/clashed sets: 10 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074373 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074373 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074373/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074373 Building REAL250005074374 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074374' /scratch/stefan/7916156/working/building/REAL250005074374 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074374 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074374/0 /scratch/stefan/7916156/working/building/REAL250005074374 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 496) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/496 `/scratch/stefan/7916156/working/3D/496' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1)=C1CC1) `REAL250005074374.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074374/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074374 none CC(C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1)=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.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, 5, 1, 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, 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, 15, 8, 15, 8, 8, 6, 7, 6, 1, 6, 1, 1, 1, 1, 1, 1, 7, 37, 37, 37, 37, 37, 37, 8, 8, 8, 8, 8, 6, 1, 8, 7, 37, 37, 37, 37] 37 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36]) total number of confs: 111 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074374 none CC(C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1)=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.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, 5, 1, 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, 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: [25, 7, 1, 7, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 8, 7, 7, 1, 25, 25, 25, 25, 25, 25, 1, 1, 2, 2, 2, 2, 8, 1, 1, 25, 25, 25, 25] 37 rigid atoms, others: [32, 2, 4, 5, 6, 7, 8, 17, 24, 25, 31] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 33, 34, 35, 36]) total number of confs: 83 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.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: REAL250005074374 none CC(C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1)=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.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, 5, 1, 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, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 10, 10, 25, 25, 25, 25, 33, 33, 33, 37, 37, 37, 37, 37, 25, 1, 1, 1, 2, 2, 2, 25, 25, 25, 25, 25, 33, 37, 25, 25, 1, 1, 1, 1] 37 rigid atoms, others: [0, 1, 2, 35, 36, 33, 34, 18, 19, 20] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 89 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074374 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074374 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074374/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074374 Building REAL250005074375 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074375' /scratch/stefan/7916156/working/building/REAL250005074375 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074375 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074375/0 /scratch/stefan/7916156/working/building/REAL250005074375 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 497) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/497 `/scratch/stefan/7916156/working/3D/497' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC1C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074375.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074375/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074375 none CC1=CC1C(=O)N1CC(C)(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'] 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, 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] 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: [25, 25, 25, 5, 1, 5, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 1, 25, 25, 25, 25, 25, 1, 1, 2, 2, 2, 2, 8, 1, 1] 39 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 19, 25, 26] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31]) total number of confs: 79 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074375 none CC1=CC1C(=O)N1CC(C)(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'] 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, 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] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 10, 10, 25, 25, 25, 25, 32, 32, 32, 39, 39, 39, 39, 39, 25, 2, 2, 2, 1, 1, 25, 25, 25, 25, 25, 32, 39, 25, 25] 39 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 93 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.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: REAL250005074375 none CC1=CC1C(=O)N1CC(C)(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'] 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, 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] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 14, 8, 14, 8, 8, 6, 7, 6, 1, 6, 1, 1, 1, 1, 1, 1, 7, 39, 39, 39, 39, 39, 8, 8, 8, 8, 8, 7, 1, 7, 7] 39 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33]) total number of confs: 117 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074375 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074375 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074375/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074375 Building REAL250005074376 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074376' /scratch/stefan/7916156/working/building/REAL250005074376 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074376 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074376/0 /scratch/stefan/7916156/working/building/REAL250005074376 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 498) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/498 `/scratch/stefan/7916156/working/3D/498' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074376.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074376/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074376 none CN(C)C(=O)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 8, 5, 1, 11, 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, 6, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 13, 17, 8, 13, 8, 8, 6, 8, 6, 1, 6, 1, 1, 1, 1, 1, 1, 8, 17, 17, 17, 17, 17, 17, 8, 8, 8, 8, 8, 6, 1, 8, 8] 17 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: 49 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074376 none CN(C)C(=O)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 8, 5, 1, 11, 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, 6, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 6, 13, 1, 6, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 1, 13, 13, 13, 13, 13, 13, 1, 1, 2, 2, 2, 3, 8, 1, 1] 17 rigid atoms, others: [34, 35, 5, 7, 8, 9, 10, 11, 20, 27, 28] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074376 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074376 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074376/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074376 Building REAL250005074377 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074377' /scratch/stefan/7916156/working/building/REAL250005074377 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074377 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074377/0 /scratch/stefan/7916156/working/building/REAL250005074377 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 499) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/499 `/scratch/stefan/7916156/working/3D/499' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(O)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074377.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074377/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074377 none CCCC(O)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 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', 'C.3', 'H', 'H', '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, 5, 7, 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, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 297 conformations in input total number of sets (complete confs): 297 using faster count positions algorithm for large data unique positions, atoms: [99, 94, 72, 27, 72, 11, 27, 11, 11, 9, 11, 9, 1, 9, 1, 1, 1, 1, 1, 1, 11, 99, 99, 99, 98, 99, 96, 96, 72, 216, 11, 11, 11, 11, 11, 10, 1, 11, 11] 297 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: 41 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074377 none CCCC(O)C(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 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', 'C.3', 'H', 'H', '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, 5, 7, 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, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 297 conformations in input total number of sets (complete confs): 297 using faster count positions algorithm for large data unique positions, atoms: [80, 66, 31, 6, 31, 1, 6, 1, 1, 1, 1, 1, 3, 3, 3, 11, 11, 11, 11, 11, 1, 80, 80, 80, 78, 80, 69, 69, 31, 93, 1, 1, 2, 2, 2, 3, 11, 1, 1] 297 rigid atoms, others: [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, 32, 33, 34, 35, 36]) total number of confs: 474 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074377 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074377 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074377/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074377 Building REAL250005074378 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074378' /scratch/stefan/7916156/working/building/REAL250005074378 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074378 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074378/0 /scratch/stefan/7916156/working/building/REAL250005074378 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 500) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/500 `/scratch/stefan/7916156/working/3D/500' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(O)CC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074378.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074378.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074378/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074378 none CCC(O)CC(=O)N1CC(C)(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 306 conformations in input total number of sets (complete confs): 306 using faster count positions algorithm for large data unique positions, atoms: [102, 94, 74, 94, 20, 10, 20, 10, 10, 8, 10, 8, 1, 8, 1, 1, 1, 1, 1, 1, 10, 102, 102, 102, 102, 102, 94, 282, 74, 74, 10, 10, 10, 10, 10, 8, 1, 10, 10] 306 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: 698 number of broken/clashed sets: 26 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074378 none CCC(O)CC(=O)N1CC(C)(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 306 conformations in input total number of sets (complete confs): 306 using faster count positions algorithm for large data unique positions, atoms: [81, 62, 38, 65, 6, 1, 6, 1, 1, 1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 10, 1, 81, 81, 81, 80, 81, 65, 195, 38, 38, 1, 1, 2, 2, 2, 3, 10, 1, 1] 306 rigid atoms, others: [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, 32, 33, 34, 35, 36]) total number of confs: 575 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074378 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074378 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074378/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074378 Building REAL250005074379 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074379' /scratch/stefan/7916156/working/building/REAL250005074379 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074379 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074379/0 /scratch/stefan/7916156/working/building/REAL250005074379 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 501) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/501 `/scratch/stefan/7916156/working/3D/501' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)CCCCF)C1) `REAL250005074379.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074379.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074379/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074379 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)CCCCF)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 15, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 142 conformations in input total number of sets (complete confs): 142 using faster count positions algorithm for large data unique positions, atoms: [10, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 10, 10, 10, 23, 23, 66, 87, 137, 141, 10, 10, 10, 10, 7, 1, 10, 10, 66, 66, 102, 102, 136, 136, 142, 142, 10, 10] 142 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 25] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 723 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074379 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)CCCCF)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 5, 5, 15, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 142 conformations in input total number of sets (complete confs): 142 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 10, 1, 1, 1, 4, 4, 26, 38, 76, 110, 1, 2, 2, 2, 3, 10, 1, 1, 26, 26, 47, 47, 74, 75, 112, 112, 1, 1] 142 rigid atoms, others: [0, 1, 2, 36, 37, 11, 12, 13, 20, 26, 27] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 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 /scratch/stefan/7916156/working/building/REAL250005074379 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074379 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074379/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074379 Building REAL250005074380 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074380' /scratch/stefan/7916156/working/building/REAL250005074380 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074380 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074380/0 /scratch/stefan/7916156/working/building/REAL250005074380 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 502) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/502 `/scratch/stefan/7916156/working/3D/502' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)[C@H]2CC(=O)N2)C1) `REAL250005074380.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074380/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074380 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)[C@H]2CC(=O)N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 6, 4, 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: [13, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 13, 13, 13, 27, 27, 50, 50, 50, 50, 50, 13, 13, 13, 13, 7, 1, 13, 13, 50, 50, 50, 13, 13] 50 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 26] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 151 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074380 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)[C@H]2CC(=O)N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 6, 4, 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: [1, 1, 1, 3, 3, 3, 13, 13, 13, 13, 13, 1, 1, 1, 6, 6, 28, 28, 28, 28, 28, 1, 2, 2, 2, 3, 13, 1, 1, 28, 28, 28, 1, 1] 50 rigid atoms, others: [0, 1, 2, 33, 32, 11, 12, 13, 21, 27, 28] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 29, 30, 31]) total number of confs: 93 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.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: REAL250005074380 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)[C@H]2CC(=O)N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 6, 4, 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: [28, 28, 28, 43, 43, 43, 50, 50, 50, 50, 50, 28, 9, 1, 9, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 43, 50, 28, 28, 1, 1, 1, 28, 28] 50 rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 29, 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, 32, 33]) total number of confs: 120 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074380 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074380 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074380/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074380 Building REAL250005074381 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074381' /scratch/stefan/7916156/working/building/REAL250005074381 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074381 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074381/0 /scratch/stefan/7916156/working/building/REAL250005074381 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 503) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/503 `/scratch/stefan/7916156/working/3D/503' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1(C(=O)N2CC(C)(NC(=O)C3=CC(=O)[N-]O3)C2)CC1) `REAL250005074381.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074381/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074381 none COC1(C(=O)N2CC(C)(NC(=O)C3=CC(=O)[N-]O3)C2)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', '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, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 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: [17, 15, 7, 1, 7, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 1, 15, 15, 17, 17, 17, 1, 1, 2, 2, 2, 3, 8, 1, 1, 15, 15, 15, 15] 24 rigid atoms, others: [32, 3, 5, 6, 7, 8, 9, 18, 24, 25, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 33, 34, 35, 36]) total number of confs: 63 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074381 none COC1(C(=O)N2CC(C)(NC(=O)C3=CC(=O)[N-]O3)C2)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', '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, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 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: [6, 1, 1, 1, 7, 7, 15, 15, 15, 15, 19, 19, 19, 23, 23, 23, 23, 23, 15, 1, 1, 6, 6, 6, 15, 15, 15, 15, 15, 19, 23, 15, 15, 1, 1, 1, 1] 24 rigid atoms, others: [1, 2, 3, 36, 35, 33, 34, 19, 20] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074381 none COC1(C(=O)N2CC(C)(NC(=O)C3=CC(=O)[N-]O3)C2)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', '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, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [24, 23, 15, 8, 15, 8, 8, 6, 8, 6, 1, 6, 1, 1, 1, 1, 1, 1, 8, 23, 23, 24, 24, 24, 8, 8, 8, 8, 8, 6, 1, 8, 8, 23, 23, 23, 23] 24 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36]) total number of confs: 71 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074381 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074381 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074381/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074381 Building REAL250005074382 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074382' /scratch/stefan/7916156/working/building/REAL250005074382 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074382 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074382/0 /scratch/stefan/7916156/working/building/REAL250005074382 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 504) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/504 `/scratch/stefan/7916156/working/3D/504' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2CSC2)C1) `REAL250005074382.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074382/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074382 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2CSC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 14, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [14, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 14, 14, 14, 30, 30, 35, 35, 35, 14, 14, 14, 14, 8, 1, 14, 14, 35, 35, 35, 35, 35, 14, 14] 35 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 24] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 111 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074382 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2CSC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 14, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 3, 3, 3, 14, 14, 14, 14, 14, 1, 1, 1, 6, 6, 18, 18, 18, 1, 2, 2, 2, 3, 14, 1, 1, 18, 18, 18, 18, 18, 1, 1] 35 rigid atoms, others: [0, 1, 2, 33, 32, 11, 12, 13, 19, 25, 26] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.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: REAL250005074382 none CC1(NC(=O)C2=CC(=O)[N-]O2)CN(C(=O)C2CSC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 5, 14, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 30, 30, 30, 35, 35, 35, 35, 35, 18, 8, 1, 8, 1, 1, 1, 1, 18, 18, 18, 18, 30, 35, 18, 18, 1, 1, 1, 1, 1, 18, 18] 35 rigid atoms, others: [13, 15, 16, 17, 18, 27, 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, 32, 33]) total number of confs: 92 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074382 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074382 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074382/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074382 Building REAL250005074383 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074383' /scratch/stefan/7916156/working/building/REAL250005074383 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074383 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074383/0 /scratch/stefan/7916156/working/building/REAL250005074383 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 505) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/505 `/scratch/stefan/7916156/working/3D/505' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074383.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074383/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074383 none C=CC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 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, 6, 7, 7, 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 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 8, 14, 8, 8, 6, 8, 6, 1, 6, 1, 1, 1, 1, 1, 1, 8, 14, 14, 14, 8, 8, 8, 8, 8, 6, 1, 8, 8] 14 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29]) total number of confs: 39 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074383 none C=CC(=O)N1CC(C)(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 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, 6, 7, 7, 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 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 1, 5, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 1, 10, 10, 10, 1, 1, 2, 2, 2, 3, 8, 1, 1] 14 rigid atoms, others: [2, 4, 5, 6, 7, 8, 17, 21, 22, 28, 29] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 23, 24, 25, 26, 27]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074383 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074383 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074383/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074383 Building REAL250005074384 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074384' /scratch/stefan/7916156/working/building/REAL250005074384 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074384 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074384/0 /scratch/stefan/7916156/working/building/REAL250005074384 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 506) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/506 `/scratch/stefan/7916156/working/3D/506' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2CC(=O)N2)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074384.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074384/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074384 none CC1(NC(=O)C2CC(=O)N2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 13, 13, 1, 13, 1, 1, 1, 1, 1, 24, 24, 24, 74, 74, 88, 88, 88, 88, 88, 24, 24, 24, 24, 13, 1, 1, 1, 1, 24, 24, 88, 24, 24] 88 rigid atoms, others: [3, 5, 6, 7, 8, 9, 25, 26, 27, 28] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33]) total number of confs: 237 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074384 none CC1(NC(=O)C2CC(=O)N2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 24, 24, 24, 24, 1, 1, 1, 6, 6, 22, 22, 22, 22, 22, 1, 2, 2, 2, 3, 24, 24, 24, 24, 1, 1, 22, 1, 1] 88 rigid atoms, others: [0, 1, 2, 33, 32, 10, 11, 12, 20, 29, 30] set([3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 31]) total number of confs: 93 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.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: REAL250005074384 none CC1(NC(=O)C2CC(=O)N2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 22, 22, 36, 36, 36, 88, 88, 88, 88, 22, 8, 1, 8, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 36, 88, 88, 88, 88, 22, 22, 1, 22, 22] 88 rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33]) total number of confs: 240 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074384 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074384 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074384/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074384 Building REAL250005074385 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074385' /scratch/stefan/7916156/working/building/REAL250005074385 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074385 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074385/0 /scratch/stefan/7916156/working/building/REAL250005074385 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 507) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/507 `/scratch/stefan/7916156/working/3D/507' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2CC(F)C2)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074385.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074385/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074385 none CC1(NC(=O)C2CC(F)C2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 15, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [20, 11, 11, 1, 11, 1, 1, 1, 1, 1, 20, 20, 20, 59, 59, 66, 66, 66, 66, 66, 20, 20, 20, 20, 11, 1, 1, 1, 1, 1, 1, 20, 20, 66, 20, 20] 66 rigid atoms, others: [3, 5, 6, 7, 8, 9, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31, 32, 33, 34, 35]) total number of confs: 179 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074385 none CC1(NC(=O)C2CC(F)C2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 15, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 3, 3, 3, 20, 20, 20, 20, 1, 1, 1, 6, 6, 21, 21, 21, 21, 21, 1, 2, 2, 2, 3, 20, 20, 20, 20, 20, 20, 1, 1, 21, 1, 1] 66 rigid atoms, others: [0, 1, 2, 35, 32, 10, 11, 12, 34, 20, 31] set([3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074385 none CC1(NC(=O)C2CC(F)C2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 15, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 34, 34, 34, 66, 66, 66, 66, 21, 10, 1, 10, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 34, 66, 66, 66, 66, 66, 66, 21, 21, 1, 21, 21] 66 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: 191 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074385 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074385 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074385/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074385 Building REAL250005074386 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074386' /scratch/stefan/7916156/working/building/REAL250005074386 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074386 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074386/0 /scratch/stefan/7916156/working/building/REAL250005074386 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 508) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/508 `/scratch/stefan/7916156/working/3D/508' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NC(=O)C2=CC=NO2)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074386.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074386/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074386 none CC1(NC(=O)C2=CC=NO2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 8, 12, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [15, 8, 8, 1, 8, 1, 1, 1, 1, 1, 15, 15, 15, 31, 31, 37, 37, 37, 37, 37, 15, 15, 15, 15, 8, 1, 1, 15, 15, 37, 15, 15] 37 rigid atoms, others: [3, 5, 6, 7, 8, 9, 25, 26] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31]) total number of confs: 103 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074386 none CC1(NC(=O)C2=CC=NO2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 8, 12, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 3, 3, 3, 15, 15, 15, 15, 1, 1, 1, 7, 7, 13, 14, 14, 14, 14, 1, 2, 2, 2, 3, 15, 15, 1, 1, 14, 1, 1] 37 rigid atoms, others: [0, 1, 2, 10, 11, 12, 20, 27, 28, 30, 31] set([3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 29]) 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.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: REAL250005074386 none CC1(NC(=O)C2=CC=NO2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 8, 12, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [14, 14, 14, 22, 22, 22, 37, 37, 37, 37, 14, 7, 1, 7, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 22, 37, 37, 14, 14, 1, 14, 14] 37 rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31]) total number of confs: 83 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074386 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074386 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074386/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074386 Building REAL250005074387 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074387' /scratch/stefan/7916156/working/building/REAL250005074387 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074387 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074387/0 /scratch/stefan/7916156/working/building/REAL250005074387 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 509) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/509 `/scratch/stefan/7916156/working/3D/509' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NC1CN(C(=O)C2=CC(=O)[N-]O2)CCC1(C)C) `REAL250005074387.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074387/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074387 none CCC(=O)NC1CN(C(=O)C2=CC(=O)[N-]O2)CCC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 3, 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 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [67, 52, 52, 52, 38, 38, 38, 12, 1, 12, 1, 1, 1, 1, 1, 1, 38, 38, 38, 38, 38, 67, 67, 67, 67, 67, 52, 38, 38, 38, 1, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38] 67 rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 202 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074387 none CCC(=O)NC1CN(C(=O)C2=CC(=O)[N-]O2)CCC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 3, 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 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [24, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 38, 38, 38, 38, 38, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 5, 1, 1, 1, 38, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2] 67 rigid atoms, others: [32, 33, 34, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 27, 28, 29, 31] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 30, 35, 36, 37, 38, 39, 40]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074387 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074387 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074387/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074387 Building REAL250005074388 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074388' /scratch/stefan/7916156/working/building/REAL250005074388 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074388 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074388/0 /scratch/stefan/7916156/working/building/REAL250005074388 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 510) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/510 `/scratch/stefan/7916156/working/3D/510' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC1CN(C(=O)C2=CC(=O)[N-]O2)CCC1(C)C) `REAL250005074388.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074388/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074388 none CC(=O)NC1CN(C(=O)C2=CC(=O)[N-]O2)CCC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 21, 21, 21, 10, 1, 10, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 23, 23, 23, 23, 21, 21, 21, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21] 23 rigid atoms, others: [7, 9, 10, 11, 12, 13, 14, 27] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 46 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074388 none CC(=O)NC1CN(C(=O)C2=CC(=O)[N-]O2)CCC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 21, 21, 21, 21, 21, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 21, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2] 23 rigid atoms, others: [3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 24, 25, 26, 28, 29, 30, 31] set([0, 1, 2, 34, 36, 33, 32, 8, 9, 10, 11, 12, 13, 14, 35, 20, 21, 22, 23, 27, 37]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074388 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074388 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074388/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074388 Building REAL250005074389 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074389' /scratch/stefan/7916156/working/building/REAL250005074389 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074389 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074389/0 /scratch/stefan/7916156/working/building/REAL250005074389 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 511) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/511 `/scratch/stefan/7916156/working/3D/511' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CCN(C(=O)C2=CC(=O)[N-]O2)CC1NC(=O)CO) `REAL250005074389.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074389/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074389 none CC1(C)CCN(C(=O)C2=CC(=O)[N-]O2)CC1NC(=O)CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 159 conformations in input total number of sets (complete confs): 159 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 33, 33, 33, 11, 1, 11, 1, 1, 1, 1, 1, 1, 33, 33, 33, 46, 46, 46, 53, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 33, 33, 33, 46, 53, 53, 159] 159 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 301 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074389 none CC1(C)CCN(C(=O)C2=CC(=O)[N-]O2)CC1NC(=O)CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 159 conformations in input total number of sets (complete confs): 159 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 7, 33, 33, 33, 33, 33, 1, 1, 1, 5, 5, 5, 28, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 33, 1, 1, 1, 5, 28, 28, 84] 159 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 34, 14, 15, 33, 24, 25, 26, 27, 28, 29, 30, 16] set([35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 31]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074389 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074389 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074389/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074389 Building REAL250005074390 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074390' /scratch/stefan/7916156/working/building/REAL250005074390 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074390 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074390/0 /scratch/stefan/7916156/working/building/REAL250005074390 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 512) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/512 `/scratch/stefan/7916156/working/3D/512' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N1CCC(C)(C)C(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074390.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074390.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074390/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074390 none CCC(=O)N1CCC(C)(C)C(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 9, 14, 9, 9, 9, 9, 9, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 9, 14, 14, 14, 14, 14, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 1, 9, 9] 14 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: 41 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074390 none CCC(=O)N1CCC(C)(C)C(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [9, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 9, 9, 9, 9, 1, 9, 9, 9, 9, 9, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 5, 9, 1, 1] 14 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 40, 20, 36, 26, 27, 28, 29, 39] set([0, 1, 3, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 56 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074390 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074390 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074390/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074390 Building REAL250005074391 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074391' /scratch/stefan/7916156/working/building/REAL250005074391 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074391 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074391/0 /scratch/stefan/7916156/working/building/REAL250005074391 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 513) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/513 `/scratch/stefan/7916156/working/3D/513' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC(C)(C)C(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074391.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074391/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074391 none CC(=O)N1CCC(C)(C)C(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [10, 8, 10, 8, 8, 8, 8, 8, 8, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 8, 10, 10, 10, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8] 10 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: 31 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074391 none CC(=O)N1CCC(C)(C)C(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 8, 8, 8, 1, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 5, 8, 1, 1] 10 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 33, 19, 23, 24, 25, 26, 37, 36] set([0, 32, 2, 34, 11, 12, 13, 14, 15, 16, 17, 18, 35, 20, 21, 22, 27, 28, 29, 30, 31]) total number of confs: 39 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074391 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074391 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074391/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074391 Building REAL250005074392 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074392' /scratch/stefan/7916156/working/building/REAL250005074392 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074392 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074392/0 /scratch/stefan/7916156/working/building/REAL250005074392 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 514) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/514 `/scratch/stefan/7916156/working/3D/514' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CCN(C(=O)CO)CC1NC(=O)C1=CC(=O)[N-]O1) `REAL250005074392.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074392/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074392 none CC1(C)CCN(C(=O)CO)CC1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 11, 11, 11, 11, 17, 17, 17, 11, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 17, 17, 51, 11, 11, 11, 6, 1] 51 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: 98 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074392 none CC1(C)CCN(C(=O)CO)CC1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 9, 1, 1, 1, 5, 5, 5, 11, 11, 11, 11, 11, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 9, 9, 27, 1, 1, 1, 5, 11] 51 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 34, 35, 24, 25, 26, 27, 28, 29, 30, 36] set([32, 33, 37, 38, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31]) total number of confs: 86 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074392 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074392 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074392/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074392 Building REAL250005074393 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074393' /scratch/stefan/7916156/working/building/REAL250005074393 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074393 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074393/0 /scratch/stefan/7916156/working/building/REAL250005074393 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 515) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/515 `/scratch/stefan/7916156/working/3D/515' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(=O)N1CCC(C)(C)C(NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074393.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074393.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074393/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074393 none C=CC(=O)N1CCC(C)(C)C(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 11, 16, 11, 11, 11, 11, 11, 11, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 11, 16, 16, 16, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 1, 11, 11] 16 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: 45 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074393 none C=CC(=O)N1CCC(C)(C)C(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [12, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 11, 11, 11, 11, 11, 1, 12, 12, 12, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 5, 11, 1, 1] 16 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 34, 38, 20, 24, 25, 26, 27, 37] set([0, 1, 3, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 28, 29, 30, 31, 32, 33, 35, 36]) total number of confs: 67 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074393 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074393 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074393/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074393 Building REAL250005074394 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074394' /scratch/stefan/7916156/working/building/REAL250005074394 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074394 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074394/0 /scratch/stefan/7916156/working/building/REAL250005074394 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 516) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/516 `/scratch/stefan/7916156/working/3D/516' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1F) `REAL250005074394.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074394/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074394 none CCC(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [81, 66, 66, 66, 38, 38, 38, 38, 11, 1, 11, 1, 1, 1, 1, 1, 1, 38, 38, 38, 81, 81, 81, 81, 81, 66, 38, 38, 38, 38, 38, 1, 38, 38, 38] 81 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]) total number of confs: 247 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074394 none CCC(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [29, 6, 6, 6, 1, 1, 1, 1, 1, 1, 7, 7, 38, 38, 38, 38, 38, 1, 1, 1, 29, 29, 29, 29, 29, 6, 1, 1, 1, 1, 1, 38, 1, 1, 1] 81 rigid atoms, others: [32, 33, 34, 4, 5, 6, 7, 8, 9, 17, 18, 19, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 31]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074394 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074394 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074394/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074394 Building REAL250005074395 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074395' /scratch/stefan/7916156/working/building/REAL250005074395 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074395 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074395/0 /scratch/stefan/7916156/working/building/REAL250005074395 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 517) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/517 `/scratch/stefan/7916156/working/3D/517' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1F) `REAL250005074395.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074395/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074395 none CC(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 26, 26, 26, 26, 11, 1, 11, 1, 1, 1, 1, 1, 1, 26, 26, 26, 29, 29, 29, 29, 26, 26, 26, 26, 26, 1, 26, 26, 26] 29 rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31]) total number of confs: 58 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074395 none CC(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 1, 1, 1, 1, 1, 1, 7, 7, 26, 26, 26, 26, 26, 1, 1, 1, 6, 6, 6, 6, 1, 1, 1, 1, 1, 26, 1, 1, 1] 29 rigid atoms, others: [3, 4, 5, 6, 7, 8, 16, 17, 18, 23, 24, 25, 26, 27, 29, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 28]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074395 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074395 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074395/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074395 Building REAL250005074396 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074396' /scratch/stefan/7916156/working/building/REAL250005074396 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074396 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074396/0 /scratch/stefan/7916156/working/building/REAL250005074396 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 518) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/518 `/scratch/stefan/7916156/working/3D/518' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1F)C1CC1) `REAL250005074396.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074396.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074396/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074396 none O=C(NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1F)C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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: [11, 1, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 15, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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 103 conformations in input total number of sets (complete confs): 103 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 35, 35, 35, 35, 12, 1, 12, 1, 1, 1, 1, 1, 1, 35, 35, 35, 65, 103, 103, 65, 35, 35, 35, 35, 35, 1, 35, 35, 35, 103, 103, 103, 103, 103] 103 rigid atoms, others: [7, 9, 10, 11, 12, 13, 14, 27] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 285 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074396 none O=C(NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1F)C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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: [11, 1, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 15, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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 103 conformations in input total number of sets (complete confs): 103 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 1, 7, 7, 35, 35, 35, 35, 35, 1, 1, 1, 6, 34, 34, 6, 1, 1, 1, 1, 1, 35, 1, 1, 1, 34, 34, 34, 34, 34] 103 rigid atoms, others: [2, 3, 4, 5, 6, 7, 15, 16, 17, 22, 23, 24, 25, 26, 28, 29, 30] set([0, 1, 34, 35, 33, 32, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 27, 31]) 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.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: REAL250005074396 none O=C(NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1F)C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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: [11, 1, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 15, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 104 conformations in input total number of sets (complete confs): 104 using faster count positions algorithm for large data unique positions, atoms: [13, 1, 13, 13, 33, 33, 33, 33, 86, 86, 104, 104, 104, 104, 104, 33, 33, 33, 1, 1, 1, 13, 33, 33, 33, 33, 33, 104, 33, 33, 33, 1, 1, 1, 1, 1] 104 rigid atoms, others: [32, 1, 34, 35, 33, 18, 19, 20, 31] 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]) total number of confs: 273 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074396 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074396 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074396/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074396 Building REAL250005074397 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074397' /scratch/stefan/7916156/working/building/REAL250005074397 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074397 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074397/0 /scratch/stefan/7916156/working/building/REAL250005074397 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 519) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/519 `/scratch/stefan/7916156/working/3D/519' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1F) `REAL250005074397.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074397/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074397 none CCCC(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1F 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', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 190 conformations in input total number of sets (complete confs): 190 using faster count positions algorithm for large data unique positions, atoms: [190, 185, 102, 102, 102, 44, 44, 44, 44, 11, 1, 11, 1, 1, 1, 1, 1, 1, 44, 44, 44, 190, 190, 190, 190, 190, 185, 185, 102, 44, 44, 44, 44, 44, 1, 44, 44, 44] 190 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]) total number of confs: 667 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074397 none CCCC(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1F 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', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 190 conformations in input total number of sets (complete confs): 190 using faster count positions algorithm for large data unique positions, atoms: [55, 41, 6, 6, 6, 1, 1, 1, 1, 1, 1, 7, 7, 44, 44, 44, 44, 44, 1, 1, 1, 65, 65, 65, 65, 65, 41, 41, 6, 1, 1, 1, 1, 1, 44, 1, 1, 1] 190 rigid atoms, others: [32, 33, 35, 36, 5, 6, 7, 8, 9, 10, 18, 19, 20, 37, 29, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 34]) total number of confs: 386 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074397 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074397 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074397/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074397 Building REAL250005074398 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074398' /scratch/stefan/7916156/working/building/REAL250005074398 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074398 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074398/0 /scratch/stefan/7916156/working/building/REAL250005074398 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 520) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/520 `/scratch/stefan/7916156/working/3D/520' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1F) `REAL250005074398.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074398/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074398 none CC(C)C(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1F 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', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [90, 81, 90, 81, 81, 40, 40, 40, 40, 12, 1, 12, 1, 1, 1, 1, 1, 1, 40, 40, 40, 90, 90, 90, 90, 90, 90, 90, 81, 40, 40, 40, 40, 40, 1, 40, 40, 40] 90 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]) total number of confs: 244 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074398 none CC(C)C(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1F 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', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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: [25, 6, 25, 6, 6, 1, 1, 1, 1, 1, 1, 7, 7, 40, 40, 40, 40, 40, 1, 1, 1, 25, 25, 25, 25, 25, 25, 25, 6, 1, 1, 1, 1, 1, 40, 1, 1, 1] 90 rigid atoms, others: [32, 33, 35, 36, 5, 6, 7, 8, 9, 10, 18, 19, 20, 37, 29, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 34]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074398 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074398 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074398/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074398 Building REAL250005074399 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074399' /scratch/stefan/7916156/working/building/REAL250005074399 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074399 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074399/0 /scratch/stefan/7916156/working/building/REAL250005074399 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 521) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/521 `/scratch/stefan/7916156/working/3D/521' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1F) `REAL250005074399.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074399/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074399 none C=CCC(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1F 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', 'F', '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, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 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, 76, 76, 76, 40, 40, 40, 40, 12, 1, 12, 1, 1, 1, 1, 1, 1, 40, 40, 40, 156, 156, 156, 156, 156, 76, 40, 40, 40, 40, 40, 1, 40, 40, 40] 156 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35]) total number of confs: 549 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074399 none C=CCC(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1F 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', 'F', '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, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 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: [67, 30, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 40, 40, 40, 40, 40, 1, 1, 1, 67, 67, 67, 30, 30, 5, 1, 1, 1, 1, 1, 40, 1, 1, 1] 156 rigid atoms, others: [33, 34, 35, 5, 6, 7, 8, 9, 10, 18, 19, 20, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 32, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26]) total number of confs: 269 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074399 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074399 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074399/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074399 Building REAL250005074400 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074400' /scratch/stefan/7916156/working/building/REAL250005074400 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074400 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074400/0 /scratch/stefan/7916156/working/building/REAL250005074400 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 522) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/522 `/scratch/stefan/7916156/working/3D/522' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CO)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1F) `REAL250005074400.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074400/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074400 none O=C(CO)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 15, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 48, 54, 26, 26, 26, 26, 10, 1, 10, 1, 1, 1, 1, 1, 1, 26, 26, 26, 54, 54, 162, 48, 26, 26, 26, 26, 26, 1, 26, 26, 26] 162 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32]) total number of confs: 324 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074400 none O=C(CO)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 15, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 26, 1, 1, 1, 1, 1, 1, 7, 7, 26, 26, 26, 26, 26, 1, 1, 1, 26, 26, 78, 6, 1, 1, 1, 1, 1, 26, 1, 1, 1] 162 rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 17, 18, 19, 24, 25, 26, 27, 28, 30, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 29]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074400 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074400 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074400/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074400 Building REAL250005074401 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074401' /scratch/stefan/7916156/working/building/REAL250005074401 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074401 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074401/0 /scratch/stefan/7916156/working/building/REAL250005074401 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 523) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/523 `/scratch/stefan/7916156/working/3D/523' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1F) `REAL250005074401.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074401/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074401 none CC=CC(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1F 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', 'F', '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, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [73, 73, 63, 63, 63, 40, 40, 40, 40, 11, 1, 11, 1, 1, 1, 1, 1, 1, 40, 40, 40, 73, 73, 73, 73, 73, 63, 40, 40, 40, 40, 40, 1, 40, 40, 40] 73 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: 185 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074401 none CC=CC(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1F 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', 'F', '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, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 6, 6, 6, 1, 1, 1, 1, 1, 1, 7, 7, 40, 40, 40, 40, 40, 1, 1, 1, 23, 23, 23, 23, 23, 6, 1, 1, 1, 1, 1, 40, 1, 1, 1] 73 rigid atoms, others: [33, 34, 35, 5, 6, 7, 8, 9, 10, 18, 19, 20, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 32, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074401 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074401 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074401/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074401 Building REAL250005074402 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074402' /scratch/stefan/7916156/working/building/REAL250005074402 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074402 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074402/0 /scratch/stefan/7916156/working/building/REAL250005074402 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 524) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/524 `/scratch/stefan/7916156/working/3D/524' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(F)C1) `REAL250005074402.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074402.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074402/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074402 none CCCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(F)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', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 38, 16, 38, 16, 16, 16, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 16, 16, 16, 55, 55, 55, 55, 55, 55, 55, 16, 16, 16, 16, 16, 8, 1, 16, 16, 16] 55 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]) total number of confs: 197 number of broken/clashed sets: 15 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074402 none CCCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(F)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', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [28, 19, 6, 1, 6, 1, 1, 1, 1, 1, 6, 6, 6, 16, 16, 16, 16, 16, 1, 1, 1, 28, 28, 28, 28, 28, 19, 19, 1, 1, 1, 1, 1, 6, 16, 1, 1, 1] 55 rigid atoms, others: [32, 35, 3, 36, 5, 6, 7, 8, 9, 18, 19, 20, 37, 28, 29, 30, 31] set([0, 1, 2, 34, 4, 33, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 150 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074402 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074402 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074402/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074402 Building REAL250005074403 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074403' /scratch/stefan/7916156/working/building/REAL250005074403 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074403 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074403/0 /scratch/stefan/7916156/working/building/REAL250005074403 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 525) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/525 `/scratch/stefan/7916156/working/3D/525' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(F)C1) `REAL250005074403.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074403/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074403 none CC(C)C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(F)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', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 10, 33, 10, 10, 10, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 10, 10, 10, 33, 33, 33, 33, 33, 33, 33, 10, 10, 10, 10, 10, 6, 1, 10, 10, 10] 33 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]) total number of confs: 87 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074403 none CC(C)C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(F)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', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [12, 7, 12, 1, 7, 1, 1, 1, 1, 1, 5, 5, 5, 10, 10, 10, 10, 10, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 5, 10, 1, 1, 1] 33 rigid atoms, others: [32, 35, 3, 36, 5, 6, 7, 8, 9, 18, 19, 20, 37, 28, 29, 30, 31] set([0, 1, 2, 34, 4, 33, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 60 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074403 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074403 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074403/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074403 Building REAL250005074404 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074404' /scratch/stefan/7916156/working/building/REAL250005074404 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074404 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074404/0 /scratch/stefan/7916156/working/building/REAL250005074404 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 526) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/526 `/scratch/stefan/7916156/working/3D/526' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(F)C1) `REAL250005074404.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074404/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074404 none CCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(F)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', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 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, 10, 27, 10, 10, 10, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 10, 10, 10, 27, 27, 27, 27, 27, 10, 10, 10, 10, 10, 6, 1, 10, 10, 10] 27 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]) total number of confs: 73 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074404 none CCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(F)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', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 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: [12, 6, 1, 6, 1, 1, 1, 1, 1, 6, 6, 6, 10, 10, 10, 10, 10, 1, 1, 1, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 6, 10, 1, 1, 1] 27 rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 34, 17, 18, 19, 25, 26, 27, 28, 29] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 30, 31]) total number of confs: 67 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074404 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074404 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074404/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074404 Building REAL250005074405 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074405' /scratch/stefan/7916156/working/building/REAL250005074405 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074405 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074405/0 /scratch/stefan/7916156/working/building/REAL250005074405 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 527) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/527 `/scratch/stefan/7916156/working/3D/527' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(F)C1) `REAL250005074405.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074405/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074405 none CC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 13, 19, 13, 13, 13, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 13, 13, 13, 19, 19, 19, 13, 13, 13, 13, 13, 10, 1, 13, 13, 13] 19 rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31]) total number of confs: 59 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074405 none CC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 1, 5, 1, 1, 1, 1, 1, 5, 5, 5, 13, 13, 13, 13, 13, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 5, 13, 1, 1, 1] 19 rigid atoms, others: [1, 3, 4, 5, 6, 7, 16, 17, 18, 22, 23, 24, 25, 26, 29, 30, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 27, 28]) total number of confs: 32 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074405 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074405 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074405/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074405 Building REAL250005074406 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074406' /scratch/stefan/7916156/working/building/REAL250005074406 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074406 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074406/0 /scratch/stefan/7916156/working/building/REAL250005074406 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 528) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/528 `/scratch/stefan/7916156/working/3D/528' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CCN(C(=O)C2CC2)CC1F)C1=CC(=O)[N-]O1) `REAL250005074406.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074406/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074406 none O=C(NC1CCN(C(=O)C2CC2)CC1F)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', 'F', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 15, 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, 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 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 13, 13, 13, 13, 8, 1, 8, 1, 1, 1, 13, 13, 13, 26, 30, 30, 30, 30, 30, 26, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 13, 13, 13, 30] 30 rigid atoms, others: [7, 9, 10, 11, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 32, 33, 34, 35]) total number of confs: 79 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074406 none O=C(NC1CCN(C(=O)C2CC2)CC1F)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', 'F', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 15, 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, 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 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 1, 1, 1, 1, 1, 1, 6, 6, 13, 13, 1, 1, 1, 5, 9, 9, 9, 9, 9, 5, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 1, 1, 1, 9] 30 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 12, 13, 14, 34, 22, 23, 24, 25, 26] set([0, 1, 35, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 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.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: REAL250005074406 none O=C(NC1CCN(C(=O)C2CC2)CC1F)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', 'F', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 15, 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, 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 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 9, 9, 9, 9, 18, 18, 30, 30, 9, 9, 9, 1, 1, 1, 1, 1, 1, 6, 9, 9, 9, 9, 9, 30, 30, 30, 30, 30, 9, 9, 9, 1] 30 rigid atoms, others: [1, 35, 15, 16, 17, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 101 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074406 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074406 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074406/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074406 Building REAL250005074407 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074407' /scratch/stefan/7916156/working/building/REAL250005074407 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074407 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074407/0 /scratch/stefan/7916156/working/building/REAL250005074407 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 529) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/529 `/scratch/stefan/7916156/working/3D/529' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CO)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(F)C1) `REAL250005074407.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074407/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074407 none O=C(CO)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(F)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 15, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [34, 16, 34, 34, 16, 16, 16, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 16, 16, 16, 34, 34, 102, 16, 16, 16, 16, 16, 7, 1, 16, 16, 16] 102 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32]) total number of confs: 203 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074407 none O=C(CO)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(F)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 15, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 15, 1, 1, 1, 1, 1, 6, 6, 6, 16, 16, 16, 16, 16, 1, 1, 1, 15, 15, 45, 1, 1, 1, 1, 1, 6, 16, 1, 1, 1] 102 rigid atoms, others: [32, 1, 4, 5, 6, 7, 8, 17, 18, 19, 23, 24, 25, 26, 27, 30, 31] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 28, 29]) total number of confs: 130 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074407 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074407 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074407/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074407 Building REAL250005074408 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074408' /scratch/stefan/7916156/working/building/REAL250005074408 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074408 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074408/0 /scratch/stefan/7916156/working/building/REAL250005074408 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 530) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/530 `/scratch/stefan/7916156/working/3D/530' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(F)C1) `REAL250005074408.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074408/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074408 none CC(=O)C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [36, 24, 36, 13, 24, 13, 13, 13, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 13, 13, 13, 36, 36, 36, 13, 13, 13, 13, 13, 7, 1, 13, 13, 13] 36 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33]) total number of confs: 121 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074408 none CC(=O)C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 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: [21, 7, 21, 1, 7, 1, 1, 1, 1, 1, 6, 6, 6, 13, 13, 13, 13, 13, 1, 1, 1, 21, 21, 21, 1, 1, 1, 1, 1, 6, 13, 1, 1, 1] 36 rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 18, 19, 20, 24, 25, 26, 27, 28, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 29, 30]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074408 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074408 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074408/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074408 Building REAL250005074409 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074409' /scratch/stefan/7916156/working/building/REAL250005074409 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074409 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074409/0 /scratch/stefan/7916156/working/building/REAL250005074409 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 531) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/531 `/scratch/stefan/7916156/working/3D/531' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(F)C1) `REAL250005074409.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074409/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074409 none CC=CC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 38, 18, 38, 18, 18, 18, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 18, 18, 18, 43, 43, 43, 43, 43, 18, 18, 18, 18, 18, 10, 1, 18, 18, 18] 43 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: 133 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074409 none CC=CC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 7, 1, 7, 1, 1, 1, 1, 1, 6, 6, 6, 18, 18, 18, 18, 18, 1, 1, 1, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 6, 18, 1, 1, 1] 43 rigid atoms, others: [33, 34, 3, 5, 6, 7, 8, 9, 18, 19, 20, 26, 27, 28, 29, 30, 35] set([0, 1, 2, 4, 32, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 31]) total number of confs: 81 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074409 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074409 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074409/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074409 Building REAL250005074410 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074410' /scratch/stefan/7916156/working/building/REAL250005074410 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074410 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074410/0 /scratch/stefan/7916156/working/building/REAL250005074410 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 532) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/532 `/scratch/stefan/7916156/working/3D/532' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(F)C1) `REAL250005074410.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074410/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074410 none C=CCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(F)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [70, 70, 49, 17, 49, 17, 17, 17, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 17, 17, 17, 70, 70, 70, 70, 70, 17, 17, 17, 17, 17, 8, 1, 17, 17, 17] 70 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: 251 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074410 none C=CCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(F)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [43, 24, 6, 1, 6, 1, 1, 1, 1, 1, 6, 6, 6, 17, 17, 17, 17, 17, 1, 1, 1, 43, 43, 43, 24, 24, 1, 1, 1, 1, 1, 6, 17, 1, 1, 1] 70 rigid atoms, others: [33, 34, 3, 5, 6, 7, 8, 9, 18, 19, 20, 26, 27, 28, 29, 30, 35] set([0, 1, 2, 4, 32, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 31]) total number of confs: 181 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074410 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074410 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074410/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074410 Building REAL250005074411 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074411' /scratch/stefan/7916156/working/building/REAL250005074411 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074411 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074411/0 /scratch/stefan/7916156/working/building/REAL250005074411 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 533) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/533 `/scratch/stefan/7916156/working/3D/533' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(F)C1) `REAL250005074411.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074411.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074411/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074411 none N#CCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(F)C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 15, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 32, 10, 32, 10, 10, 10, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 10, 10, 10, 55, 55, 10, 10, 10, 10, 10, 6, 1, 10, 10, 10] 55 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32]) total number of confs: 193 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074411 none N#CCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(F)C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 15, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 6, 1, 6, 1, 1, 1, 1, 1, 6, 6, 6, 10, 10, 10, 10, 10, 1, 1, 1, 22, 22, 1, 1, 1, 1, 1, 6, 10, 1, 1, 1] 55 rigid atoms, others: [32, 3, 5, 6, 7, 8, 9, 18, 19, 20, 23, 24, 25, 26, 27, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 28, 29]) total number of confs: 97 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074411 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074411 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074411/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074411 Building REAL250005074412 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074412' /scratch/stefan/7916156/working/building/REAL250005074412 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074412 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074412/0 /scratch/stefan/7916156/working/building/REAL250005074412 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 534) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/534 `/scratch/stefan/7916156/working/3D/534' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(F)C1) `REAL250005074412.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074412/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074412 none C=CC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(F)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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, 28, 14, 28, 14, 14, 14, 8, 7, 1, 7, 1, 1, 1, 1, 1, 1, 14, 14, 14, 28, 28, 28, 14, 14, 14, 14, 14, 8, 1, 14, 14, 14] 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, 32]) total number of confs: 85 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074412 none C=CC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(F)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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: [13, 7, 1, 7, 1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 14, 14, 1, 1, 1, 13, 13, 13, 1, 1, 1, 1, 1, 6, 14, 1, 1, 1] 28 rigid atoms, others: [32, 2, 4, 5, 6, 7, 8, 17, 18, 19, 23, 24, 25, 26, 27, 30, 31] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 28, 29]) total number of confs: 61 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074412 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074412 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074412/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074412 Building REAL250005074413 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074413' /scratch/stefan/7916156/working/building/REAL250005074413 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074413 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074413/0 /scratch/stefan/7916156/working/building/REAL250005074413 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 535) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/535 `/scratch/stefan/7916156/working/3D/535' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NC1CCC2CC1CN2C(=O)C1=CC(=O)[N-]O1) `REAL250005074413.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074413.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074413/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074413 none CCC(=O)NC1CCC2CC1CN2C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [46, 36, 36, 36, 23, 23, 23, 22, 22, 23, 23, 23, 9, 1, 9, 1, 1, 1, 1, 1, 1, 46, 46, 46, 46, 46, 36, 23, 23, 23, 23, 23, 22, 23, 23, 23, 23, 23, 1] 46 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: 156 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074413 none CCC(=O)NC1CCC2CC1CN2C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [22, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22] 46 rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 37, 36, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 38, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074413 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074413 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074413/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074413 Building REAL250005074414 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074414' /scratch/stefan/7916156/working/building/REAL250005074414 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074414 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074414/0 /scratch/stefan/7916156/working/building/REAL250005074414 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 536) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/536 `/scratch/stefan/7916156/working/3D/536' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC1CCC2CC1CN2C(=O)C1=CC(=O)[N-]O1) `REAL250005074414.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074414/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074414 none CC(=O)NC1CCC2CC1CN2C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 9, 9, 9, 8, 8, 9, 9, 9, 5, 1, 5, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 9, 9, 9, 8, 8, 8, 9, 9, 9, 9, 9, 1] 12 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: 30 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074414 none CC(=O)NC1CCC2CC1CN2C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 8, 8, 8, 8, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8] 12 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 35, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23]) total number of confs: 26 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074414 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074414 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074414/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074414 Building REAL250005074415 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074415' /scratch/stefan/7916156/working/building/REAL250005074415 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074415 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074415/0 /scratch/stefan/7916156/working/building/REAL250005074415 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 537) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/537 `/scratch/stefan/7916156/working/3D/537' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CO)NC1CCC2CC1CN2C(=O)C1=CC(=O)[N-]O1) `REAL250005074415.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074415.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074415/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074415 none O=C(CO)NC1CCC2CC1CN2C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 30, 33, 17, 17, 17, 16, 16, 17, 17, 17, 8, 1, 8, 1, 1, 1, 1, 1, 1, 33, 33, 99, 30, 17, 17, 17, 17, 17, 16, 17, 17, 17, 17, 17, 1] 99 rigid atoms, others: [36, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 200 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074415 none O=C(CO)NC1CCC2CC1CN2C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 16, 16, 16, 16, 16, 18, 18, 54, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16] 99 rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 36, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074415 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074415 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074415/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074415 Building REAL250005074416 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074416' /scratch/stefan/7916156/working/building/REAL250005074416 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074416 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074416/0 /scratch/stefan/7916156/working/building/REAL250005074416 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 538) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/538 `/scratch/stefan/7916156/working/3D/538' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N1CC2CC1CCC2NC(=O)C1=CC(=O)[N-]O1) `REAL250005074416.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074416/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074416 none CCC(=O)N1CC2CC1CCC2NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 18, 10, 18, 10, 10, 10, 10, 10, 10, 10, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 1] 19 rigid atoms, others: [38, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 55 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074416 none CCC(=O)N1CC2CC1CCC2NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [11, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 10, 10, 10, 10, 10, 12, 12, 12, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 10] 19 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 10, 11, 12, 34, 36, 26, 27, 28, 29, 30, 31] set([0, 1, 3, 37, 38, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074416 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074416 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074416/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074416 Building REAL250005074417 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074417' /scratch/stefan/7916156/working/building/REAL250005074417 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074417 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074417/0 /scratch/stefan/7916156/working/building/REAL250005074417 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 539) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/539 `/scratch/stefan/7916156/working/3D/539' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC2CC1CCC2NC(=O)C1=CC(=O)[N-]O1) `REAL250005074417.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074417.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074417/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074417 none CC(=O)N1CC2CC1CCC2NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 7, 5, 5, 5, 5, 5, 5, 5, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 7, 7, 7, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 1] 7 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: 21 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074417 none CC(=O)N1CC2CC1CCC2NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 5, 5, 5, 5, 5, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 5] 7 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 33, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 35, 2, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22]) total number of confs: 23 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074417 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074417 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074417/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074417 Building REAL250005074418 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074418' /scratch/stefan/7916156/working/building/REAL250005074418 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074418 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074418/0 /scratch/stefan/7916156/working/building/REAL250005074418 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 540) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/540 `/scratch/stefan/7916156/working/3D/540' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CO)N1CC2CC1CCC2NC(=O)C1=CC(=O)[N-]O1) `REAL250005074418.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074418.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074418/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074418 none O=C(CO)N1CC2CC1CCC2NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [17, 13, 17, 19, 13, 13, 13, 13, 13, 13, 13, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 19, 19, 57, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 1] 57 rigid atoms, others: [36, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 118 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074418 none O=C(CO)N1CC2CC1CCC2NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 13, 13, 13, 13, 13, 9, 9, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 13] 57 rigid atoms, others: [32, 1, 34, 33, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 35, 2, 3, 36, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23]) total number of confs: 80 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074418 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074418 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074418/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074418 Building REAL250005074419 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074419' /scratch/stefan/7916156/working/building/REAL250005074419 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074419 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074419/0 /scratch/stefan/7916156/working/building/REAL250005074419 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 541) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/541 `/scratch/stefan/7916156/working/3D/541' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(=O)N1CC2CC1CCC2NC(=O)C1=CC(=O)[N-]O1) `REAL250005074419.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074419/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074419 none C=CC(=O)N1CC2CC1CCC2NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 9, 14, 9, 9, 9, 9, 9, 9, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 14, 14, 14, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 1] 14 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: 39 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074419 none C=CC(=O)N1CC2CC1CCC2NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [10, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 9, 9, 9, 9, 9, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 9] 14 rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 34, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 3, 36, 35, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074419 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074419 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074419/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074419 Building REAL250005074420 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074420' /scratch/stefan/7916156/working/building/REAL250005074420 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074420 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074420/0 /scratch/stefan/7916156/working/building/REAL250005074420 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 542) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/542 `/scratch/stefan/7916156/working/3D/542' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NCC1CCCCN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074420.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074420/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074420 none CCC(=O)NCC1CCCCN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [49, 30, 30, 30, 26, 12, 12, 12, 12, 12, 12, 7, 1, 7, 1, 1, 1, 1, 1, 1, 12, 49, 49, 49, 49, 49, 30, 26, 26, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 12, 12] 49 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: 217 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074420 none CCC(=O)NCC1CCCCN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 16, 16, 16, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 12, 12, 12, 12, 12, 1, 34, 34, 34, 34, 34, 16, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 12, 40, 37, 20, 39, 29, 30, 31] set([0, 1, 2, 3, 4, 38, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074420 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074420 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074420/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074420 Building REAL250005074421 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074421' /scratch/stefan/7916156/working/building/REAL250005074421 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074421 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074421/0 /scratch/stefan/7916156/working/building/REAL250005074421 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 543) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/543 `/scratch/stefan/7916156/working/3D/543' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC1CCCCN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074421.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074421/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074421 none CC(=O)NCC1CCCCN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 15, 15, 15, 15, 15, 15, 7, 1, 7, 1, 1, 1, 1, 1, 1, 15, 28, 28, 28, 28, 28, 28, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 15, 15] 28 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: 91 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074421 none CC(=O)NCC1CCCCN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 6, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 15, 15, 15, 15, 15, 1, 14, 14, 14, 14, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1] 28 rigid atoms, others: [32, 33, 34, 4, 5, 6, 7, 8, 9, 10, 11, 37, 19, 36, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 35, 20, 21, 22, 23, 24, 25]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074421 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074421 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074421/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074421 Building REAL250005074422 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074422' /scratch/stefan/7916156/working/building/REAL250005074422 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074422 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074422/0 /scratch/stefan/7916156/working/building/REAL250005074422 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 544) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/544 `/scratch/stefan/7916156/working/3D/544' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CO)NCC1CCCCN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074422.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074422/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074422 none O=C(CO)NCC1CCCCN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 12, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 204 conformations in input total number of sets (complete confs): 204 using faster count positions algorithm for large data unique positions, atoms: [66, 66, 66, 68, 48, 18, 18, 18, 18, 18, 18, 9, 1, 9, 1, 1, 1, 1, 1, 1, 18, 68, 68, 204, 66, 48, 48, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 18, 18] 204 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: 445 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074422 none O=C(CO)NCC1CCCCN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 12, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 204 conformations in input total number of sets (complete confs): 204 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 25, 43, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 18, 18, 18, 18, 18, 1, 43, 43, 129, 25, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 1, 1] 204 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 10, 11, 12, 38, 37, 20, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 36]) total number of confs: 311 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074422 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074422 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074422/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074422 Building REAL250005074423 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074423' /scratch/stefan/7916156/working/building/REAL250005074423 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074423 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074423/0 /scratch/stefan/7916156/working/building/REAL250005074423 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 545) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/545 `/scratch/stefan/7916156/working/3D/545' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N1CCCCC(CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074423.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074423/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074423 none CCC(=O)N1CCCCC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [97, 96, 60, 96, 60, 60, 60, 60, 60, 25, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 60, 97, 97, 97, 97, 97, 60, 60, 60, 60, 60, 60, 60, 60, 60, 25, 25, 6, 1, 60, 60] 97 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: 302 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074423 none CCC(=O)N1CCCCC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [17, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 10, 44, 44, 44, 60, 60, 60, 60, 60, 1, 18, 18, 18, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 44, 60, 1, 1] 97 rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 9, 10, 39, 34, 40, 20, 26, 27, 28, 29, 30, 31] set([0, 1, 3, 36, 37, 35, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 38]) total number of confs: 213 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074423 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074423 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074423/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074423 Building REAL250005074424 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074424' /scratch/stefan/7916156/working/building/REAL250005074424 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074424 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074424/0 /scratch/stefan/7916156/working/building/REAL250005074424 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 546) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/546 `/scratch/stefan/7916156/working/3D/546' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCCCC(CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074424.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074424/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074424 none CC(=O)N1CCCCC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [63, 55, 63, 55, 55, 55, 55, 55, 27, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 55, 63, 63, 63, 55, 55, 55, 55, 55, 55, 55, 55, 55, 27, 27, 7, 1, 55, 55] 63 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: 200 number of broken/clashed sets: 34 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074424 none CC(=O)N1CCCCC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 10, 43, 43, 43, 55, 55, 55, 55, 55, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 43, 55, 1, 1] 63 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 36, 37, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 32, 2, 34, 33, 10, 11, 12, 13, 14, 15, 16, 17, 18, 35, 20, 21, 22]) total number of confs: 149 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074424 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074424 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074424/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074424 Building REAL250005074425 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074425' /scratch/stefan/7916156/working/building/REAL250005074425 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074425 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074425/0 /scratch/stefan/7916156/working/building/REAL250005074425 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 547) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/547 `/scratch/stefan/7916156/working/3D/547' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CO)N1CCCCC(CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074425.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074425.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074425/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074425 none O=C(CO)N1CCCCC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 12, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [48, 41, 48, 50, 41, 41, 41, 41, 41, 14, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 41, 50, 50, 150, 41, 41, 41, 41, 41, 41, 41, 41, 41, 14, 14, 5, 1, 41, 41] 150 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: 311 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074425 none O=C(CO)N1CCCCC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 12, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 10, 1, 1, 1, 1, 1, 1, 1, 9, 34, 34, 34, 41, 41, 41, 41, 41, 1, 10, 10, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 34, 41, 1, 1] 150 rigid atoms, others: [32, 1, 4, 5, 6, 7, 8, 9, 10, 38, 37, 20, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 33, 2, 3, 36, 35, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 34]) total number of confs: 168 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074425 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074425 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074425/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074425 Building REAL250005074426 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074426' /scratch/stefan/7916156/working/building/REAL250005074426 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074426 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074426/0 /scratch/stefan/7916156/working/building/REAL250005074426 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 548) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/548 `/scratch/stefan/7916156/working/3D/548' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(=O)N1CCCCC(CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074426.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074426/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074426 none C=CC(=O)N1CCCCC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [75, 75, 56, 75, 56, 56, 56, 56, 56, 20, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 56, 75, 75, 75, 56, 56, 56, 56, 56, 56, 56, 56, 56, 19, 19, 5, 1, 56, 56] 75 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: 232 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074426 none C=CC(=O)N1CCCCC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [23, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 10, 45, 45, 45, 56, 56, 56, 56, 56, 1, 23, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 45, 56, 1, 1] 75 rigid atoms, others: [32, 2, 4, 5, 6, 7, 8, 9, 10, 38, 37, 20, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 34, 3, 36, 35, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23]) total number of confs: 198 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074426 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074426 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074426/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074426 Building REAL250005074427 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074427' /scratch/stefan/7916156/working/building/REAL250005074427 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074427 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074427/0 /scratch/stefan/7916156/working/building/REAL250005074427 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 549) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/549 `/scratch/stefan/7916156/working/3D/549' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074427.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074427.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074427/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074427 none CCC(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [75, 60, 60, 60, 41, 24, 41, 41, 24, 24, 11, 1, 11, 1, 1, 1, 1, 1, 1, 24, 75, 75, 75, 75, 75, 60, 41, 41, 41, 24, 24, 24, 1, 24, 24] 75 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: 278 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074427 none CCC(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 17, 17, 17, 6, 1, 6, 6, 1, 1, 1, 1, 5, 5, 24, 24, 24, 24, 24, 1, 44, 44, 44, 44, 44, 17, 6, 6, 6, 1, 1, 1, 24, 1, 1] 75 rigid atoms, others: [33, 34, 5, 8, 9, 10, 11, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 7, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32]) total number of confs: 197 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074427 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074427 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074427/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074427 Building REAL250005074428 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074428' /scratch/stefan/7916156/working/building/REAL250005074428 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074428 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074428/0 /scratch/stefan/7916156/working/building/REAL250005074428 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 550) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/550 `/scratch/stefan/7916156/working/3D/550' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074428.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074428/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074428 none COCCC(=O)N[C@@H](C)C1CN(C(=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', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 180, 78, 78, 78, 37, 21, 37, 37, 21, 21, 9, 1, 9, 1, 1, 1, 1, 1, 1, 21, 201, 201, 201, 201, 201, 180, 180, 78, 37, 37, 37, 21, 21, 21, 1, 21, 21] 201 rigid atoms, others: [36, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 807 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074428 none COCCC(=O)N[C@@H](C)C1CN(C(=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', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 120, 76, 16, 16, 16, 6, 1, 6, 6, 1, 1, 1, 1, 6, 6, 21, 21, 21, 21, 21, 1, 154, 154, 154, 120, 120, 76, 76, 16, 6, 6, 6, 1, 1, 1, 21, 1, 1] 201 rigid atoms, others: [33, 34, 35, 37, 38, 7, 10, 11, 12, 13, 21] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36]) total number of confs: 595 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074428 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074428 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074428/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074428 Building REAL250005074429 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074429' /scratch/stefan/7916156/working/building/REAL250005074429 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074429 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074429/0 /scratch/stefan/7916156/working/building/REAL250005074429 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 551) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/551 `/scratch/stefan/7916156/working/3D/551' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074429.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074429/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074429 none CC(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 23, 16, 23, 23, 16, 16, 11, 1, 11, 1, 1, 1, 1, 1, 1, 16, 26, 26, 26, 26, 23, 23, 23, 16, 16, 16, 1, 16, 16] 26 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]) total number of confs: 76 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074429 none CC(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 10, 10, 5, 1, 5, 5, 1, 1, 1, 1, 6, 6, 16, 16, 16, 16, 16, 1, 10, 10, 10, 10, 5, 5, 5, 1, 1, 1, 16, 1, 1] 26 rigid atoms, others: [4, 7, 8, 9, 10, 18, 26, 27, 28, 30, 31] set([0, 1, 2, 3, 5, 6, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 29]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074429 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074429 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074429/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074429 Building REAL250005074430 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074430' /scratch/stefan/7916156/working/building/REAL250005074430 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074430 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074430/0 /scratch/stefan/7916156/working/building/REAL250005074430 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 552) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/552 `/scratch/stefan/7916156/working/3D/552' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)C1CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074430.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074430/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074430 none C[C@H](NC(=O)C1CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 98 conformations in input total number of sets (complete confs): 98 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 13, 13, 13, 57, 57, 1, 1, 1, 1, 6, 6, 27, 27, 27, 27, 27, 1, 6, 6, 6, 13, 57, 57, 57, 57, 57, 1, 1, 1, 27, 1, 1] 98 rigid atoms, others: [32, 1, 34, 35, 9, 10, 11, 12, 20, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33]) total number of confs: 188 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074430 none C[C@H](NC(=O)C1CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [35, 11, 35, 11, 1, 11, 1, 1, 1, 35, 56, 56, 56, 85, 85, 97, 97, 97, 97, 97, 56, 35, 35, 35, 11, 1, 1, 1, 1, 1, 56, 56, 56, 97, 56, 56] 97 rigid atoms, others: [4, 6, 7, 8, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31, 32, 33, 34, 35]) total number of confs: 314 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.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: REAL250005074430 none C[C@H](NC(=O)C1CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [46, 27, 46, 46, 60, 60, 60, 97, 97, 27, 27, 10, 1, 10, 1, 1, 1, 1, 1, 1, 27, 46, 46, 46, 60, 97, 97, 97, 97, 97, 27, 27, 27, 1, 27, 27] 97 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: 307 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074430 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074430 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074430/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074430 Building REAL250005074431 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074431' /scratch/stefan/7916156/working/building/REAL250005074431 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074431 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074431/0 /scratch/stefan/7916156/working/building/REAL250005074431 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 553) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/553 `/scratch/stefan/7916156/working/3D/553' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)C1CCC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074431.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074431/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074431 none C[C@H](NC(=O)C1CCC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 15, 15, 15, 63, 63, 63, 1, 1, 1, 1, 6, 6, 25, 25, 25, 25, 25, 1, 6, 6, 6, 15, 63, 63, 63, 63, 63, 63, 63, 1, 1, 1, 25, 1, 1] 116 rigid atoms, others: [1, 34, 35, 37, 38, 33, 10, 11, 12, 13, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36]) total number of confs: 200 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074431 none C[C@H](NC(=O)C1CCC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [39, 12, 39, 12, 1, 12, 1, 1, 1, 1, 39, 63, 63, 63, 101, 101, 116, 116, 116, 116, 116, 63, 39, 39, 39, 12, 1, 1, 1, 1, 1, 1, 1, 63, 63, 63, 116, 63, 63] 116 rigid atoms, others: [32, 4, 6, 7, 8, 9, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 33, 34, 35, 36, 37, 38]) total number of confs: 378 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.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: REAL250005074431 none C[C@H](NC(=O)C1CCC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [47, 26, 47, 47, 70, 70, 70, 116, 116, 116, 26, 25, 8, 1, 8, 1, 1, 1, 1, 1, 1, 25, 47, 47, 47, 70, 116, 116, 116, 116, 116, 116, 116, 26, 26, 25, 1, 25, 25] 116 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: 384 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074431 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074431 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074431/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074431 Building REAL250005074432 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074432' /scratch/stefan/7916156/working/building/REAL250005074432 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074432 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074432/0 /scratch/stefan/7916156/working/building/REAL250005074432 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 554) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/554 `/scratch/stefan/7916156/working/3D/554' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)CC1CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074432.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074432.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074432/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074432 none C[C@H](NC(=O)CC1CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 17, 17, 17, 94, 135, 135, 1, 1, 1, 1, 6, 6, 30, 30, 30, 30, 30, 1, 6, 6, 6, 17, 94, 94, 135, 135, 135, 135, 135, 1, 1, 1, 30, 1, 1] 201 rigid atoms, others: [1, 34, 35, 37, 38, 33, 10, 11, 12, 13, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36]) total number of confs: 528 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074432 none C[C@H](NC(=O)CC1CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [78, 25, 78, 25, 3, 25, 1, 1, 1, 1, 78, 135, 135, 135, 182, 182, 201, 201, 201, 201, 201, 135, 78, 78, 78, 25, 3, 3, 1, 1, 1, 1, 1, 135, 135, 135, 201, 135, 135] 201 rigid atoms, others: [32, 6, 7, 8, 9, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35, 36, 37, 38]) 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.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: REAL250005074432 none C[C@H](NC(=O)CC1CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [61, 31, 61, 61, 102, 102, 102, 168, 201, 201, 30, 30, 11, 1, 11, 1, 1, 1, 1, 1, 1, 30, 61, 61, 61, 102, 168, 168, 201, 201, 201, 201, 201, 31, 30, 30, 1, 30, 30] 201 rigid atoms, others: [36, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 779 number of broken/clashed sets: 9 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074432 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074432 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074432/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074432 Building REAL250005074433 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074433' /scratch/stefan/7916156/working/building/REAL250005074433 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074433 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074433/0 /scratch/stefan/7916156/working/building/REAL250005074433 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 555) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/555 `/scratch/stefan/7916156/working/3D/555' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)C(C)(C)F)C1CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074433.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074433/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074433 none C[C@H](NC(=O)C(C)(C)F)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 5, 5, 15, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [36, 22, 36, 36, 53, 53, 53, 77, 77, 77, 22, 22, 10, 1, 10, 1, 1, 1, 1, 1, 1, 22, 36, 36, 36, 53, 77, 77, 77, 77, 77, 77, 22, 22, 22, 1, 22, 22] 77 rigid atoms, others: [35, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37]) total number of confs: 283 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074433 none C[C@H](NC(=O)C(C)(C)F)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 5, 5, 15, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 15, 15, 15, 56, 56, 56, 1, 1, 1, 1, 6, 6, 22, 22, 22, 22, 22, 1, 6, 6, 6, 15, 56, 56, 56, 56, 56, 56, 1, 1, 1, 22, 1, 1] 77 rigid atoms, others: [32, 1, 34, 36, 37, 33, 10, 11, 12, 13, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35]) total number of confs: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074433 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074433 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074433/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074433 Building REAL250005074434 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074434' /scratch/stefan/7916156/working/building/REAL250005074434 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074434 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074434/0 /scratch/stefan/7916156/working/building/REAL250005074434 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 556) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/556 `/scratch/stefan/7916156/working/3D/556' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074434.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074434/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074434 none COCC(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 72, 72, 72, 42, 25, 42, 42, 25, 25, 10, 1, 10, 1, 1, 1, 1, 1, 1, 25, 124, 124, 124, 124, 124, 72, 42, 42, 42, 25, 25, 25, 1, 25, 25] 124 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: 470 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074434 none COCC(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [86, 70, 16, 16, 16, 6, 1, 6, 6, 1, 1, 1, 1, 6, 6, 25, 25, 25, 25, 25, 1, 86, 86, 86, 70, 70, 16, 6, 6, 6, 1, 1, 1, 25, 1, 1] 124 rigid atoms, others: [32, 34, 35, 6, 9, 10, 11, 12, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33]) total number of confs: 314 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074434 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074434 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074434/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074434 Building REAL250005074435 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074435' /scratch/stefan/7916156/working/building/REAL250005074435 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074435 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074435/0 /scratch/stefan/7916156/working/building/REAL250005074435 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 557) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/557 `/scratch/stefan/7916156/working/3D/557' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074435.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074435/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074435 none CCCC(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 167 conformations in input total number of sets (complete confs): 167 using faster count positions algorithm for large data unique positions, atoms: [167, 153, 102, 102, 102, 52, 32, 52, 52, 32, 32, 12, 1, 12, 1, 1, 1, 1, 1, 1, 32, 167, 167, 167, 167, 167, 153, 153, 102, 52, 52, 52, 32, 32, 32, 1, 32, 32] 167 rigid atoms, others: [35, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37]) total number of confs: 636 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074435 none CCCC(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [101, 71, 17, 17, 17, 6, 1, 6, 6, 1, 1, 1, 1, 6, 6, 32, 32, 32, 32, 32, 1, 110, 110, 110, 110, 110, 71, 71, 17, 6, 6, 6, 1, 1, 1, 32, 1, 1] 167 rigid atoms, others: [32, 33, 34, 36, 37, 6, 9, 10, 11, 12, 20] set([0, 1, 2, 3, 4, 5, 7, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35]) total number of confs: 559 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074435 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074435 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074435/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074435 Building REAL250005074436 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074436' /scratch/stefan/7916156/working/building/REAL250005074436 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074436 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074436/0 /scratch/stefan/7916156/working/building/REAL250005074436 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 558) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/558 `/scratch/stefan/7916156/working/3D/558' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074436.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074436.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074436/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074436 none CC(C)CC(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 104, 105, 60, 60, 60, 35, 23, 35, 35, 23, 23, 11, 1, 11, 1, 1, 1, 1, 1, 1, 23, 105, 105, 105, 105, 105, 105, 105, 104, 104, 60, 35, 35, 35, 23, 23, 23, 1, 23, 23] 105 rigid atoms, others: [38, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40]) total number of confs: 414 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074436 none CC(C)CC(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [51, 47, 56, 16, 16, 16, 5, 1, 5, 5, 1, 1, 1, 1, 6, 6, 23, 23, 23, 23, 23, 1, 56, 56, 56, 56, 56, 56, 56, 47, 47, 16, 5, 5, 5, 1, 1, 1, 23, 1, 1] 105 rigid atoms, others: [35, 36, 37, 7, 40, 10, 11, 12, 13, 21, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38]) total number of confs: 289 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074436 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074436 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074436/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074436 Building REAL250005074437 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074437' /scratch/stefan/7916156/working/building/REAL250005074437 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074437 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074437/0 /scratch/stefan/7916156/working/building/REAL250005074437 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 559) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/559 `/scratch/stefan/7916156/working/3D/559' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)C1CC1C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074437.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074437/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074437 none C[C@H](NC(=O)C1CC1C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 112 conformations in input total number of sets (complete confs): 112 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 15, 15, 15, 64, 64, 64, 1, 1, 1, 1, 7, 7, 25, 25, 25, 25, 25, 1, 6, 6, 6, 15, 64, 64, 64, 64, 64, 64, 64, 1, 1, 1, 25, 1, 1] 112 rigid atoms, others: [1, 34, 35, 37, 38, 33, 10, 11, 12, 13, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36]) total number of confs: 202 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074437 none C[C@H](NC(=O)C1CC1C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 112 conformations in input total number of sets (complete confs): 112 using faster count positions algorithm for large data unique positions, atoms: [41, 13, 41, 13, 1, 13, 1, 1, 1, 1, 41, 64, 64, 64, 99, 99, 112, 112, 112, 112, 112, 64, 41, 41, 41, 13, 1, 1, 1, 1, 2, 2, 2, 64, 64, 64, 112, 64, 64] 112 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, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 377 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.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: REAL250005074437 none C[C@H](NC(=O)C1CC1C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 112 conformations in input total number of sets (complete confs): 112 using faster count positions algorithm for large data unique positions, atoms: [50, 25, 50, 50, 67, 67, 67, 112, 112, 112, 25, 25, 9, 1, 9, 1, 1, 1, 1, 1, 1, 25, 50, 50, 50, 67, 112, 112, 112, 112, 112, 112, 112, 25, 25, 25, 1, 25, 25] 112 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: 367 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074437 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074437 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074437/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074437 Building REAL250005074438 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074438' /scratch/stefan/7916156/working/building/REAL250005074438 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074438 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074438/0 /scratch/stefan/7916156/working/building/REAL250005074438 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 560) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/560 `/scratch/stefan/7916156/working/3D/560' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCC(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074438.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074438/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074438 none CCOCC(=O)N[C@@H](C)C1CN(C(=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', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 124, 75, 75, 75, 41, 25, 41, 41, 25, 25, 10, 1, 10, 1, 1, 1, 1, 1, 1, 25, 132, 132, 132, 132, 132, 124, 124, 75, 41, 41, 41, 25, 25, 25, 1, 25, 25] 132 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: 477 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074438 none CCOCC(=O)N[C@@H](C)C1CN(C(=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', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [104, 99, 58, 16, 16, 16, 6, 1, 6, 6, 1, 1, 1, 1, 6, 6, 25, 25, 25, 25, 25, 1, 104, 104, 104, 104, 104, 58, 58, 16, 6, 6, 6, 1, 1, 1, 25, 1, 1] 132 rigid atoms, others: [33, 34, 35, 37, 38, 7, 10, 11, 12, 13, 21] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36]) total number of confs: 346 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074438 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074438 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074438/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074438 Building REAL250005074439 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074439' /scratch/stefan/7916156/working/building/REAL250005074439 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074439 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074439/0 /scratch/stefan/7916156/working/building/REAL250005074439 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 561) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/561 `/scratch/stefan/7916156/working/3D/561' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)=CC(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074439.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074439.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074439/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074439 none CC(C)=CC(=O)N[C@@H](C)C1CN(C(=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', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [74, 74, 74, 54, 54, 54, 33, 21, 33, 33, 21, 21, 8, 1, 8, 1, 1, 1, 1, 1, 1, 21, 74, 74, 74, 74, 74, 74, 74, 54, 33, 33, 33, 21, 21, 21, 1, 21, 21] 74 rigid atoms, others: [36, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 249 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074439 none CC(C)=CC(=O)N[C@@H](C)C1CN(C(=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', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [41, 41, 41, 15, 15, 15, 5, 1, 5, 5, 1, 1, 1, 1, 7, 7, 21, 21, 21, 21, 21, 1, 41, 41, 41, 41, 41, 41, 41, 15, 5, 5, 5, 1, 1, 1, 21, 1, 1] 74 rigid atoms, others: [33, 34, 35, 37, 38, 7, 10, 11, 12, 13, 21] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074439 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074439 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074439/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074439 Building REAL250005074440 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074440' /scratch/stefan/7916156/working/building/REAL250005074440 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074440 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074440/0 /scratch/stefan/7916156/working/building/REAL250005074440 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 562) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/562 `/scratch/stefan/7916156/working/3D/562' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSCC(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074440.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074440/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074440 none CSCC(=O)N[C@@H](C)C1CN(C(=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', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 87, 87, 87, 45, 26, 45, 45, 26, 26, 11, 1, 11, 1, 1, 1, 1, 1, 1, 26, 201, 201, 201, 182, 182, 87, 45, 45, 45, 26, 26, 26, 1, 26, 26] 201 rigid atoms, others: [33, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35]) total number of confs: 748 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074440 none CSCC(=O)N[C@@H](C)C1CN(C(=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', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 91, 15, 15, 15, 6, 1, 6, 6, 1, 1, 1, 1, 6, 6, 26, 26, 26, 26, 26, 1, 143, 149, 149, 91, 91, 15, 6, 6, 6, 1, 1, 1, 26, 1, 1] 201 rigid atoms, others: [32, 34, 35, 6, 9, 10, 11, 12, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33]) total number of confs: 453 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074440 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074440 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074440/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074440 Building REAL250005074441 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074441' /scratch/stefan/7916156/working/building/REAL250005074441 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074441 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074441/0 /scratch/stefan/7916156/working/building/REAL250005074441 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 563) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/563 `/scratch/stefan/7916156/working/3D/563' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074441.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074441/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074441 none CCCCC(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [200, 198, 184, 76, 76, 76, 35, 17, 35, 35, 17, 17, 6, 1, 6, 1, 1, 1, 1, 1, 1, 17, 200, 201, 201, 201, 201, 199, 199, 184, 184, 76, 35, 35, 35, 17, 17, 17, 1, 17, 17] 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, 39, 40]) total number of confs: 826 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074441 none CCCCC(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 99, 80, 16, 16, 16, 6, 1, 6, 6, 1, 1, 1, 1, 6, 6, 17, 17, 17, 17, 17, 1, 145, 147, 147, 142, 143, 111, 111, 80, 80, 16, 6, 6, 6, 1, 1, 1, 17, 1, 1] 201 rigid atoms, others: [35, 36, 37, 7, 40, 10, 11, 12, 13, 21, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38]) total number of confs: 723 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074441 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074441 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074441/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074441 Building REAL250005074442 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074442' /scratch/stefan/7916156/working/building/REAL250005074442 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074442 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074442/0 /scratch/stefan/7916156/working/building/REAL250005074442 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 564) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/564 `/scratch/stefan/7916156/working/3D/564' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074442.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074442/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074442 none CC(C)C(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [89, 71, 89, 71, 71, 48, 26, 48, 48, 26, 26, 11, 1, 11, 1, 1, 1, 1, 1, 1, 26, 89, 89, 89, 89, 89, 89, 89, 71, 48, 48, 48, 26, 26, 26, 1, 26, 26] 89 rigid atoms, others: [35, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37]) total number of confs: 322 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074442 none CC(C)C(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [56, 18, 56, 18, 18, 6, 1, 6, 6, 1, 1, 1, 1, 6, 6, 26, 26, 26, 26, 26, 1, 56, 56, 56, 56, 56, 56, 56, 18, 6, 6, 6, 1, 1, 1, 26, 1, 1] 89 rigid atoms, others: [32, 33, 34, 36, 37, 6, 9, 10, 11, 12, 20] set([0, 1, 2, 3, 4, 5, 7, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35]) total number of confs: 241 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074442 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074442 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074442/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074442 Building REAL250005074443 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074443' /scratch/stefan/7916156/working/building/REAL250005074443 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074443 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074443/0 /scratch/stefan/7916156/working/building/REAL250005074443 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 565) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/565 `/scratch/stefan/7916156/working/3D/565' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)C(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074443.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074443.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074443/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074443 none CCC(C)C(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 123, 75, 123, 75, 75, 36, 21, 36, 36, 21, 21, 11, 1, 11, 1, 1, 1, 1, 1, 1, 21, 129, 129, 129, 129, 129, 123, 123, 123, 123, 75, 36, 36, 36, 21, 21, 21, 1, 21, 21] 129 rigid atoms, others: [38, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40]) total number of confs: 510 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074443 none CCC(C)C(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [73, 62, 15, 62, 15, 15, 5, 1, 5, 5, 1, 1, 1, 1, 6, 6, 21, 21, 21, 21, 21, 1, 78, 78, 78, 78, 78, 62, 62, 62, 62, 15, 5, 5, 5, 1, 1, 1, 21, 1, 1] 129 rigid atoms, others: [35, 36, 37, 7, 40, 10, 11, 12, 13, 21, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38]) total number of confs: 371 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074443 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074443 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074443/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074443 Building REAL250005074444 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074444' /scratch/stefan/7916156/working/building/REAL250005074444 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074444 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074444/0 /scratch/stefan/7916156/working/building/REAL250005074444 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 566) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/566 `/scratch/stefan/7916156/working/3D/566' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)C(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074444.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074444.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074444/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074444 none COC(C)C(=O)N[C@@H](C)C1CN(C(=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', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [89, 89, 67, 89, 67, 67, 37, 20, 37, 37, 20, 20, 9, 1, 9, 1, 1, 1, 1, 1, 1, 20, 89, 89, 89, 89, 89, 89, 89, 67, 37, 37, 37, 20, 20, 20, 1, 20, 20] 89 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: 328 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074444 none COC(C)C(=O)N[C@@H](C)C1CN(C(=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', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [62, 53, 16, 53, 16, 16, 6, 1, 6, 6, 1, 1, 1, 1, 7, 7, 20, 20, 20, 20, 20, 1, 62, 62, 62, 53, 53, 53, 53, 16, 6, 6, 6, 1, 1, 1, 20, 1, 1] 89 rigid atoms, others: [33, 34, 35, 37, 38, 7, 10, 11, 12, 13, 21] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36]) total number of confs: 235 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074444 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074444 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074444/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074444 Building REAL250005074445 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074445' /scratch/stefan/7916156/working/building/REAL250005074445 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074445 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074445/0 /scratch/stefan/7916156/working/building/REAL250005074445 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 567) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/567 `/scratch/stefan/7916156/working/3D/567' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCC(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074445.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074445/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074445 none C=CCCC(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 186, 76, 76, 76, 34, 18, 34, 34, 18, 18, 6, 1, 6, 1, 1, 1, 1, 1, 1, 18, 201, 201, 201, 201, 201, 186, 186, 76, 34, 34, 34, 18, 18, 18, 1, 18, 18] 201 rigid atoms, others: [36, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 802 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074445 none C=CCCC(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 121, 80, 15, 15, 15, 5, 1, 5, 5, 1, 1, 1, 1, 6, 6, 18, 18, 18, 18, 18, 1, 164, 164, 164, 121, 121, 80, 80, 15, 5, 5, 5, 1, 1, 1, 18, 1, 1] 201 rigid atoms, others: [33, 34, 35, 37, 38, 7, 10, 11, 12, 13, 21] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36]) total number of confs: 689 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074445 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074445 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074445/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074445 Building REAL250005074446 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074446' /scratch/stefan/7916156/working/building/REAL250005074446 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074446 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074446/0 /scratch/stefan/7916156/working/building/REAL250005074446 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 568) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/568 `/scratch/stefan/7916156/working/3D/568' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=C(C)C(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074446.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074446/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074446 none CC=C(C)C(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 65, 104, 65, 65, 45, 25, 45, 45, 25, 25, 10, 1, 10, 1, 1, 1, 1, 1, 1, 25, 104, 104, 104, 104, 104, 104, 104, 65, 45, 45, 45, 25, 25, 25, 1, 25, 25] 104 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: 346 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074446 none CC=C(C)C(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [59, 59, 15, 59, 15, 15, 6, 1, 6, 6, 1, 1, 1, 1, 7, 7, 25, 25, 25, 25, 25, 1, 59, 59, 59, 59, 59, 59, 59, 15, 6, 6, 6, 1, 1, 1, 25, 1, 1] 104 rigid atoms, others: [33, 34, 35, 37, 38, 7, 10, 11, 12, 13, 21] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36]) total number of confs: 194 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074446 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074446 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074446/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074446 Building REAL250005074447 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074447' /scratch/stefan/7916156/working/building/REAL250005074447 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074447 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074447/0 /scratch/stefan/7916156/working/building/REAL250005074447 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 569) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/569 `/scratch/stefan/7916156/working/3D/569' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)C1(C)CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074447.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074447.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074447/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074447 none C[C@H](NC(=O)C1(C)CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 13, 13, 13, 47, 47, 47, 1, 1, 1, 1, 6, 6, 23, 23, 23, 23, 23, 1, 6, 6, 6, 13, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 23, 1, 1] 101 rigid atoms, others: [1, 34, 35, 37, 38, 33, 10, 11, 12, 13, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36]) total number of confs: 162 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074447 none C[C@H](NC(=O)C1(C)CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [27, 7, 27, 7, 1, 7, 1, 1, 1, 1, 27, 47, 47, 47, 84, 84, 101, 101, 101, 101, 101, 47, 27, 27, 27, 7, 2, 2, 2, 1, 1, 1, 1, 47, 47, 47, 101, 47, 47] 101 rigid atoms, others: [32, 4, 6, 7, 8, 9, 29, 30, 31] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38]) total number of confs: 330 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.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: REAL250005074447 none C[C@H](NC(=O)C1(C)CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [37, 23, 37, 37, 49, 49, 49, 101, 101, 101, 23, 23, 10, 1, 10, 1, 1, 1, 1, 1, 1, 23, 37, 37, 37, 49, 101, 101, 101, 101, 101, 101, 101, 23, 23, 23, 1, 23, 23] 101 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: 327 number of broken/clashed sets: 12 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074447 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074447 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074447/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074447 Building REAL250005074448 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074448' /scratch/stefan/7916156/working/building/REAL250005074448 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074448 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074448/0 /scratch/stefan/7916156/working/building/REAL250005074448 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 570) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/570 `/scratch/stefan/7916156/working/3D/570' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@H]1C[C@H]1C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074448.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074448.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074448/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074448 none C[C@H](NC(=O)[C@@H]1C[C@H]1C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 114 conformations in input total number of sets (complete confs): 114 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 15, 15, 15, 62, 62, 62, 62, 62, 1, 1, 1, 1, 6, 6, 26, 26, 27, 26, 26, 1, 6, 6, 6, 15, 62, 62, 62, 62, 62, 1, 1, 1, 27, 1, 1] 114 rigid atoms, others: [1, 34, 35, 37, 38, 33, 12, 13, 14, 15, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36]) total number of confs: 202 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074448 none C[C@H](NC(=O)[C@@H]1C[C@H]1C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 114 conformations in input total number of sets (complete confs): 114 using faster count positions algorithm for large data unique positions, atoms: [35, 13, 35, 13, 1, 13, 1, 1, 1, 1, 1, 1, 35, 62, 62, 62, 96, 96, 114, 114, 114, 114, 114, 62, 35, 35, 35, 13, 1, 1, 2, 2, 2, 62, 62, 62, 114, 62, 62] 114 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, 35, 36, 37, 38]) total number of confs: 368 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.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: REAL250005074448 none C[C@H](NC(=O)[C@@H]1C[C@H]1C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 114 conformations in input total number of sets (complete confs): 114 using faster count positions algorithm for large data unique positions, atoms: [46, 27, 46, 46, 64, 64, 64, 114, 114, 114, 114, 114, 27, 27, 9, 1, 9, 1, 1, 1, 1, 1, 1, 26, 46, 46, 46, 64, 114, 114, 114, 114, 114, 27, 27, 27, 1, 26, 27] 114 rigid atoms, others: [36, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 364 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074448 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074448 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074448/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074448 Building REAL250005074449 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074449' /scratch/stefan/7916156/working/building/REAL250005074449 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074449 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074449/0 /scratch/stefan/7916156/working/building/REAL250005074449 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 571) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/571 `/scratch/stefan/7916156/working/3D/571' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(F)C(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074449.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074449.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074449/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074449 none CCC(F)C(=O)N[C@@H](C)C1CN(C(=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', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 7, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 133, 89, 133, 89, 89, 45, 26, 45, 45, 26, 26, 11, 1, 11, 1, 1, 1, 1, 1, 1, 26, 143, 143, 143, 143, 143, 133, 89, 45, 45, 45, 26, 26, 26, 1, 26, 26] 143 rigid atoms, others: [35, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37]) total number of confs: 564 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074449 none CCC(F)C(=O)N[C@@H](C)C1CN(C(=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', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 7, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [94, 73, 19, 73, 19, 19, 6, 1, 6, 6, 1, 1, 1, 1, 6, 6, 26, 26, 26, 26, 26, 1, 99, 99, 99, 99, 99, 73, 19, 6, 6, 6, 1, 1, 1, 26, 1, 1] 143 rigid atoms, others: [32, 33, 34, 36, 37, 7, 10, 11, 12, 13, 21] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35]) total number of confs: 468 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074449 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074449 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074449/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074449 Building REAL250005074450 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074450' /scratch/stefan/7916156/working/building/REAL250005074450 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074450 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074450/0 /scratch/stefan/7916156/working/building/REAL250005074450 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 572) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/572 `/scratch/stefan/7916156/working/3D/572' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)CCCF)C1CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074450.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074450/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074450 none C[C@H](NC(=O)CCCF)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 5, 5, 15, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 16, 31, 31, 64, 64, 64, 176, 192, 201, 16, 16, 6, 1, 6, 1, 1, 1, 1, 1, 1, 16, 31, 31, 31, 64, 176, 176, 201, 201, 201, 201, 16, 16, 16, 1, 16, 16] 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, 36, 37]) total number of confs: 872 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074450 none C[C@H](NC(=O)CCCF)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 5, 5, 15, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 15, 15, 15, 84, 104, 160, 1, 1, 1, 1, 6, 6, 16, 16, 16, 16, 16, 1, 5, 5, 5, 15, 84, 84, 124, 124, 153, 152, 1, 1, 1, 16, 1, 1] 201 rigid atoms, others: [32, 1, 34, 36, 37, 33, 10, 11, 12, 13, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35]) total number of confs: 804 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074450 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074450 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074450/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074450 Building REAL250005074451 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074451' /scratch/stefan/7916156/working/building/REAL250005074451 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074451 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074451/0 /scratch/stefan/7916156/working/building/REAL250005074451 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 573) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/573 `/scratch/stefan/7916156/working/3D/573' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@H]1C[C@@H]1C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074451.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074451/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074451 none C[C@H](NC(=O)[C@H]1C[C@@H]1C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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: [5, 1, 5, 5, 14, 14, 14, 58, 58, 58, 58, 58, 1, 1, 1, 1, 6, 6, 21, 21, 21, 21, 21, 1, 5, 5, 5, 14, 58, 58, 58, 58, 58, 1, 1, 1, 21, 1, 1] 101 rigid atoms, others: [1, 34, 35, 37, 38, 33, 12, 13, 14, 15, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36]) total number of confs: 181 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074451 none C[C@H](NC(=O)[C@H]1C[C@@H]1C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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: [36, 12, 36, 12, 1, 12, 1, 1, 1, 1, 1, 1, 36, 58, 58, 58, 86, 86, 101, 101, 101, 101, 101, 58, 36, 36, 36, 12, 1, 1, 2, 2, 2, 58, 58, 58, 101, 58, 58] 101 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, 35, 36, 37, 38]) total number of confs: 339 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074451 none C[C@H](NC(=O)[C@H]1C[C@@H]1C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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: [36, 22, 36, 36, 51, 51, 51, 101, 101, 101, 101, 101, 21, 21, 9, 1, 9, 1, 1, 1, 1, 1, 1, 21, 36, 36, 36, 51, 101, 101, 101, 101, 101, 21, 21, 21, 1, 21, 21] 101 rigid atoms, others: [36, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 316 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074451 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074451 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074451/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074451 Building REAL250005074452 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074452' /scratch/stefan/7916156/working/building/REAL250005074452 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074452 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074452/0 /scratch/stefan/7916156/working/building/REAL250005074452 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 574) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/574 `/scratch/stefan/7916156/working/3D/574' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)C(N)=O)C1CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074452.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074452/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074452 none C[C@H](NC(=O)C(N)=O)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 8, 11, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 4, 6, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [31, 22, 31, 31, 42, 42, 42, 45, 45, 22, 22, 9, 1, 9, 1, 1, 1, 1, 1, 1, 22, 31, 31, 31, 42, 45, 45, 22, 22, 22, 1, 22, 22] 45 rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32]) total number of confs: 133 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074452 none C[C@H](NC(=O)C(N)=O)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 8, 11, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 4, 6, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 13, 13, 13, 26, 26, 1, 1, 1, 1, 7, 7, 22, 22, 22, 22, 22, 1, 6, 6, 6, 13, 26, 26, 1, 1, 1, 22, 1, 1] 45 rigid atoms, others: [32, 1, 9, 10, 11, 12, 20, 27, 28, 29, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 30]) total number of confs: 112 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074452 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074452 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074452/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074452 Building REAL250005074453 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074453' /scratch/stefan/7916156/working/building/REAL250005074453 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074453 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074453/0 /scratch/stefan/7916156/working/building/REAL250005074453 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 575) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/575 `/scratch/stefan/7916156/working/3D/575' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)C(C)(C)C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074453.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074453/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074453 none C[C@H](NC(=O)C(C)(C)C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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', '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, 7, 8, 1, 11, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [30, 19, 30, 30, 33, 33, 33, 41, 41, 41, 19, 19, 7, 1, 7, 1, 1, 1, 1, 1, 1, 19, 30, 30, 30, 33, 41, 41, 41, 41, 41, 41, 41, 41, 41, 19, 19, 19, 1, 19, 19] 41 rigid atoms, others: [38, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40]) total number of confs: 151 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074453 none C[C@H](NC(=O)C(C)(C)C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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', '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, 7, 8, 1, 11, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 12, 12, 12, 18, 18, 18, 1, 1, 1, 1, 7, 7, 19, 19, 19, 19, 19, 1, 6, 6, 6, 12, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 19, 1, 1] 41 rigid atoms, others: [1, 35, 36, 37, 39, 40, 10, 11, 12, 13, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38]) total number of confs: 99 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074453 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074453 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074453/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074453 Building REAL250005074454 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074454' /scratch/stefan/7916156/working/building/REAL250005074454 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074454 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074454/0 /scratch/stefan/7916156/working/building/REAL250005074454 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 576) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/576 `/scratch/stefan/7916156/working/3D/576' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074454.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074454/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074454 none C=CCC(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 72, 72, 72, 42, 26, 42, 42, 26, 26, 11, 1, 11, 1, 1, 1, 1, 1, 1, 26, 143, 143, 143, 143, 143, 72, 42, 42, 42, 26, 26, 26, 1, 26, 26] 143 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: 545 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074454 none C=CCC(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [105, 75, 15, 15, 15, 6, 1, 6, 6, 1, 1, 1, 1, 6, 6, 26, 26, 26, 26, 26, 1, 105, 105, 105, 75, 75, 15, 6, 6, 6, 1, 1, 1, 26, 1, 1] 143 rigid atoms, others: [32, 34, 35, 6, 9, 10, 11, 12, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33]) total number of confs: 400 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074454 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074454 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074454/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074454 Building REAL250005074455 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074455' /scratch/stefan/7916156/working/building/REAL250005074455 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005074455 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074455/0 /scratch/stefan/7916156/working/building/REAL250005074455 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 577) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/577 `/scratch/stefan/7916156/working/3D/577' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)C[NH+](C)C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074455.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074455/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074455 none C[C@H](NC(=O)C[NH+](C)C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [11, 8, 11, 11, 14, 14, 14, 17, 17, 17, 17, 8, 8, 6, 1, 6, 1, 1, 1, 1, 1, 1, 8, 11, 11, 11, 14, 17, 17, 17, 17, 17, 17, 17, 17, 8, 8, 8, 1, 8, 8] 17 rigid atoms, others: [38, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40]) total number of confs: 57 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074455 none C[C@H](NC(=O)C[NH+](C)C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 9, 9, 9, 15, 15, 15, 15, 1, 1, 1, 1, 3, 3, 8, 8, 8, 8, 8, 1, 4, 4, 4, 9, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 8, 1, 1] 17 rigid atoms, others: [1, 35, 36, 37, 39, 40, 11, 12, 13, 14, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074455 /scratch/stefan/7916156/working /scratch/stefan/7916156 mkdir: created directory `1' /scratch/stefan/7916156/working/building/REAL250005074455/1 /scratch/stefan/7916156/working/building/REAL250005074455 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 1 (index: 578) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/578 `/scratch/stefan/7916156/working/3D/578' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)CN(C)C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074455.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005074455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074455/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074455 none C[C@H](NC(=O)CN(C)C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 10, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [35, 20, 35, 35, 68, 68, 68, 116, 118, 118, 20, 20, 10, 1, 10, 1, 1, 1, 1, 1, 1, 20, 35, 35, 35, 68, 116, 116, 118, 118, 118, 118, 118, 118, 20, 20, 20, 1, 20, 20] 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, 38, 39]) total number of confs: 455 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074455 none C[C@H](NC(=O)CN(C)C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 10, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 15, 15, 15, 59, 69, 69, 1, 1, 1, 1, 5, 5, 20, 20, 20, 20, 20, 1, 6, 6, 6, 15, 59, 59, 69, 69, 69, 69, 69, 69, 1, 1, 1, 20, 1, 1] 118 rigid atoms, others: [1, 34, 35, 36, 38, 39, 10, 11, 12, 13, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37]) total number of confs: 282 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074455 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074455 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 1: /scratch/stefan/7916156/working/building/REAL250005074455/1.* 0: /scratch/stefan/7916156/working/building/REAL250005074455/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074455 Building REAL250005074456 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074456' /scratch/stefan/7916156/working/building/REAL250005074456 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074456 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074456/0 /scratch/stefan/7916156/working/building/REAL250005074456 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 579) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/579 `/scratch/stefan/7916156/working/3D/579' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(O)C(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074456.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074456/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074456 none C=CC(O)C(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 324 conformations in input total number of sets (complete confs): 324 using faster count positions algorithm for large data unique positions, atoms: [108, 108, 71, 108, 71, 71, 42, 22, 42, 42, 22, 22, 10, 1, 10, 1, 1, 1, 1, 1, 1, 22, 108, 108, 108, 108, 324, 71, 42, 42, 42, 22, 22, 22, 1, 22, 22] 324 rigid atoms, others: [34, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36]) total number of confs: 736 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074456 none C=CC(O)C(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 324 conformations in input total number of sets (complete confs): 324 using faster count positions algorithm for large data unique positions, atoms: [78, 61, 18, 61, 18, 18, 7, 1, 7, 7, 1, 1, 1, 1, 6, 6, 22, 22, 22, 22, 22, 1, 78, 78, 78, 61, 183, 18, 7, 7, 7, 1, 1, 1, 22, 1, 1] 324 rigid atoms, others: [32, 33, 35, 36, 7, 10, 11, 12, 13, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34]) total number of confs: 492 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074456 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074456 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074456/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074456 Building REAL250005074457 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074457' /scratch/stefan/7916156/working/building/REAL250005074457 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074457 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074457/0 /scratch/stefan/7916156/working/building/REAL250005074457 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 580) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/580 `/scratch/stefan/7916156/working/3D/580' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)C1COC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074457.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074457.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074457/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074457 none C[C@H](NC(=O)C1COC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 5, 12, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 16, 16, 16, 57, 57, 57, 1, 1, 1, 1, 7, 7, 28, 28, 28, 28, 28, 1, 6, 6, 6, 16, 57, 57, 57, 57, 57, 1, 1, 1, 28, 1, 1] 100 rigid atoms, others: [32, 1, 35, 36, 33, 10, 11, 12, 13, 21, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34]) total number of confs: 192 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074457 none C[C@H](NC(=O)C1COC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 5, 12, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [35, 10, 35, 10, 1, 10, 1, 1, 1, 1, 35, 57, 57, 57, 90, 90, 100, 100, 100, 100, 100, 57, 35, 35, 35, 10, 1, 1, 1, 1, 1, 57, 57, 57, 100, 57, 57] 100 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, 33, 34, 35, 36]) total number of confs: 328 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.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: REAL250005074457 none C[C@H](NC(=O)C1COC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 5, 12, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [47, 28, 47, 47, 62, 62, 62, 100, 100, 100, 28, 28, 10, 1, 10, 1, 1, 1, 1, 1, 1, 28, 47, 47, 47, 62, 100, 100, 100, 100, 100, 28, 28, 28, 1, 28, 28] 100 rigid atoms, others: [34, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36]) total number of confs: 313 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074457 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074457 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074457/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074457 Building REAL250005074458 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074458' /scratch/stefan/7916156/working/building/REAL250005074458 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074458 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074458/0 /scratch/stefan/7916156/working/building/REAL250005074458 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 581) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/581 `/scratch/stefan/7916156/working/3D/581' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](C)C(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074458.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074458/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074458 none CO[C@H](C)C(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 1, 11, 8, 5, 7, 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, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [109, 109, 71, 109, 109, 71, 71, 44, 24, 44, 44, 24, 24, 10, 1, 10, 1, 1, 1, 1, 1, 1, 24, 109, 109, 109, 109, 109, 109, 71, 44, 44, 44, 24, 24, 24, 1, 24, 24] 109 rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 420 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074458 none CO[C@H](C)C(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 1, 11, 8, 5, 7, 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, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [80, 67, 15, 67, 67, 15, 15, 6, 1, 6, 6, 1, 1, 1, 1, 6, 6, 24, 24, 24, 24, 24, 1, 80, 80, 80, 67, 67, 67, 15, 6, 6, 6, 1, 1, 1, 24, 1, 1] 109 rigid atoms, others: [33, 34, 35, 37, 38, 8, 11, 12, 13, 14, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36]) total number of confs: 299 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074458 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074458 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074458/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074458 Building REAL250005074459 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074459' /scratch/stefan/7916156/working/building/REAL250005074459 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074459 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074459/0 /scratch/stefan/7916156/working/building/REAL250005074459 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 582) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/582 `/scratch/stefan/7916156/working/3D/582' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC=CC(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074459.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074459/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074459 none CCC=CC(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 168, 168, 108, 108, 108, 65, 31, 65, 65, 31, 31, 12, 1, 12, 1, 1, 1, 1, 1, 1, 31, 201, 201, 201, 201, 201, 168, 168, 108, 65, 65, 65, 31, 31, 31, 1, 31, 31] 201 rigid atoms, others: [36, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 773 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074459 none CCC=CC(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [113, 71, 71, 18, 18, 18, 6, 1, 6, 6, 1, 1, 1, 1, 7, 7, 31, 31, 31, 31, 31, 1, 113, 113, 113, 113, 113, 71, 71, 18, 6, 6, 6, 1, 1, 1, 31, 1, 1] 201 rigid atoms, others: [33, 34, 35, 37, 38, 7, 10, 11, 12, 13, 21] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36]) total number of confs: 460 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074459 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074459 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074459/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074459 Building REAL250005074460 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074460' /scratch/stefan/7916156/working/building/REAL250005074460 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types Protomer extracton resulted in 0 protomers Marking REAL250005074460 as failed and skipping /scratch/stefan/7916156/working /scratch/stefan/7916156 `/scratch/stefan/7916156/working/building/REAL250005074460' -> `/scratch/stefan/7916156/failed/REAL250005074460' Building REAL250005074461 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074461' /scratch/stefan/7916156/working/building/REAL250005074461 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074461 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074461/0 /scratch/stefan/7916156/working/building/REAL250005074461 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 583) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/583 `/scratch/stefan/7916156/working/3D/583' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)CO)C1CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074461.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074461/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074461 none C[C@H](NC(=O)CO)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [33, 23, 33, 33, 41, 41, 41, 43, 23, 23, 11, 1, 11, 1, 1, 1, 1, 1, 1, 23, 33, 33, 33, 41, 43, 43, 129, 23, 23, 23, 1, 23, 23] 129 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32]) total number of confs: 262 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074461 none C[C@H](NC(=O)CO)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 13, 13, 13, 28, 1, 1, 1, 1, 6, 6, 23, 23, 23, 23, 23, 1, 5, 5, 5, 13, 28, 28, 84, 1, 1, 1, 23, 1, 1] 129 rigid atoms, others: [32, 1, 8, 9, 10, 11, 19, 27, 28, 29, 31] set([0, 2, 3, 4, 5, 6, 7, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 30]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074461 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074461 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074461/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074461 Building REAL250005074462 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074462' /scratch/stefan/7916156/working/building/REAL250005074462 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074462 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074462/0 /scratch/stefan/7916156/working/building/REAL250005074462 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 584) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/584 `/scratch/stefan/7916156/working/3D/584' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)C(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074462.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074462.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074462/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074462 none CC(O)C(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 195 conformations in input total number of sets (complete confs): 195 using faster count positions algorithm for large data unique positions, atoms: [65, 50, 65, 50, 50, 35, 23, 35, 35, 23, 23, 12, 1, 12, 1, 1, 1, 1, 1, 1, 23, 65, 65, 65, 65, 195, 50, 35, 35, 35, 23, 23, 23, 1, 23, 23] 195 rigid atoms, others: [33, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35]) total number of confs: 425 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074462 none CC(O)C(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 195 conformations in input total number of sets (complete confs): 195 using faster count positions algorithm for large data unique positions, atoms: [42, 16, 41, 16, 16, 6, 1, 6, 6, 1, 1, 1, 1, 6, 6, 23, 23, 23, 23, 23, 1, 42, 42, 42, 42, 126, 16, 6, 6, 6, 1, 1, 1, 23, 1, 1] 195 rigid atoms, others: [32, 34, 35, 6, 9, 10, 11, 12, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33]) total number of confs: 304 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074462 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074462 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074462/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074462 Building REAL250005074463 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074463' /scratch/stefan/7916156/working/building/REAL250005074463 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074463 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074463/0 /scratch/stefan/7916156/working/building/REAL250005074463 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 585) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/585 `/scratch/stefan/7916156/working/3D/585' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)C1CC1F)C1CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074463.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074463.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074463/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074463 none C[C@H](NC(=O)C1CC1F)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 5, 5, 15, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 15, 15, 15, 65, 65, 65, 1, 1, 1, 1, 6, 6, 22, 22, 22, 22, 22, 1, 6, 6, 6, 15, 65, 65, 65, 65, 1, 1, 1, 23, 1, 1] 101 rigid atoms, others: [32, 1, 34, 35, 10, 11, 12, 13, 21, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 33]) total number of confs: 202 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074463 none C[C@H](NC(=O)C1CC1F)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 5, 5, 15, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [43, 12, 43, 12, 1, 12, 1, 1, 1, 1, 43, 65, 65, 65, 93, 93, 101, 101, 101, 101, 101, 65, 43, 43, 43, 12, 1, 1, 1, 1, 65, 65, 65, 101, 65, 65] 101 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, 32, 33, 34, 35]) total number of confs: 334 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.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: REAL250005074463 none C[C@H](NC(=O)C1CC1F)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 5, 5, 15, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [42, 23, 42, 42, 55, 55, 55, 101, 101, 101, 23, 23, 8, 1, 8, 1, 1, 1, 1, 1, 1, 22, 42, 42, 42, 55, 101, 101, 101, 101, 23, 23, 23, 1, 22, 22] 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, 34, 35]) total number of confs: 314 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074463 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074463 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074463/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074463 Building REAL250005074464 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074464' /scratch/stefan/7916156/working/building/REAL250005074464 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074464 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074464/0 /scratch/stefan/7916156/working/building/REAL250005074464 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 586) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/586 `/scratch/stefan/7916156/working/3D/586' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)CCF)C1CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074464.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074464/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074464 none C[C@H](NC(=O)CCF)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 5, 15, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 158 conformations in input total number of sets (complete confs): 158 using faster count positions algorithm for large data unique positions, atoms: [47, 26, 47, 47, 92, 92, 92, 158, 158, 26, 26, 10, 1, 10, 1, 1, 1, 1, 1, 1, 26, 47, 47, 47, 92, 158, 158, 158, 158, 26, 26, 26, 1, 26, 26] 158 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: 592 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074464 none C[C@H](NC(=O)CCF)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 5, 15, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 158 conformations in input total number of sets (complete confs): 158 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 18, 18, 18, 76, 106, 1, 1, 1, 1, 6, 6, 26, 26, 26, 26, 26, 1, 7, 7, 7, 18, 76, 76, 106, 106, 1, 1, 1, 26, 1, 1] 158 rigid atoms, others: [1, 34, 33, 9, 10, 11, 12, 20, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 32]) total number of confs: 470 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074464 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074464 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074464/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074464 Building REAL250005074465 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074465' /scratch/stefan/7916156/working/building/REAL250005074465 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074465 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074465/0 /scratch/stefan/7916156/working/building/REAL250005074465 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 587) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/587 `/scratch/stefan/7916156/working/3D/587' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)C=CCF)C1CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074465.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074465/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074465 none C[C@H](NC(=O)C=CCF)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 5, 15, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [42, 18, 42, 42, 68, 68, 68, 99, 99, 108, 18, 18, 7, 1, 7, 1, 1, 1, 1, 1, 1, 18, 42, 42, 42, 68, 99, 99, 108, 108, 18, 18, 18, 1, 18, 18] 108 rigid atoms, others: [33, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35]) total number of confs: 384 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074465 none C[C@H](NC(=O)C=CCF)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 5, 15, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 18, 18, 18, 53, 53, 86, 1, 1, 1, 1, 7, 7, 18, 18, 18, 18, 18, 1, 6, 6, 6, 18, 53, 53, 86, 86, 1, 1, 1, 18, 1, 1] 108 rigid atoms, others: [32, 1, 34, 35, 10, 11, 12, 13, 21, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 33]) total number of confs: 356 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074465 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074465 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074465/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074465 Building REAL250005074466 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074466' /scratch/stefan/7916156/working/building/REAL250005074466 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074466 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074466/0 /scratch/stefan/7916156/working/building/REAL250005074466 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 588) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/588 `/scratch/stefan/7916156/working/3D/588' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCC(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074466.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074466.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074466/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074466 none C#CCCC(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 192 conformations in input total number of sets (complete confs): 192 using faster count positions algorithm for large data unique positions, atoms: [192, 192, 182, 86, 86, 86, 46, 27, 46, 46, 27, 27, 12, 1, 12, 1, 1, 1, 1, 1, 1, 27, 192, 192, 192, 182, 182, 86, 46, 46, 46, 27, 27, 27, 1, 27, 27] 192 rigid atoms, others: [34, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36]) total number of confs: 748 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074466 none C#CCCC(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [120, 120, 84, 17, 17, 17, 6, 1, 6, 6, 1, 1, 1, 1, 6, 6, 27, 27, 27, 27, 27, 1, 120, 120, 120, 84, 84, 17, 6, 6, 6, 1, 1, 1, 27, 1, 1] 192 rigid atoms, others: [32, 33, 35, 36, 7, 10, 11, 12, 13, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34]) total number of confs: 528 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074466 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074466 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074466/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074466 Building REAL250005074467 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074467' /scratch/stefan/7916156/working/building/REAL250005074467 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074467 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074467/0 /scratch/stefan/7916156/working/building/REAL250005074467 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 589) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/589 `/scratch/stefan/7916156/working/3D/589' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)C1CCO1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074467.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074467/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074467 none C[C@H](NC(=O)C1CCO1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 5, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 13, 13, 13, 33, 33, 33, 1, 1, 1, 1, 5, 5, 18, 18, 18, 18, 18, 1, 6, 6, 6, 13, 33, 33, 33, 33, 33, 1, 1, 1, 18, 1, 1] 52 rigid atoms, others: [32, 1, 35, 36, 33, 10, 11, 12, 13, 21, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34]) total number of confs: 119 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074467 none C[C@H](NC(=O)C1CCO1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 5, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [23, 10, 23, 10, 1, 10, 1, 1, 1, 1, 23, 33, 33, 33, 43, 43, 52, 52, 52, 52, 52, 33, 23, 23, 23, 10, 1, 1, 1, 1, 1, 33, 33, 33, 52, 33, 33] 52 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, 33, 34, 35, 36]) total number of confs: 169 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.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: REAL250005074467 none C[C@H](NC(=O)C1CCO1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 5, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [33, 19, 33, 33, 44, 44, 44, 52, 52, 52, 19, 18, 9, 1, 9, 1, 1, 1, 1, 1, 1, 19, 33, 33, 33, 44, 52, 52, 52, 52, 52, 19, 18, 18, 1, 19, 19] 52 rigid atoms, others: [34, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36]) total number of confs: 166 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074467 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074467 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074467/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074467 Building REAL250005074468 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074468' /scratch/stefan/7916156/working/building/REAL250005074468 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074468 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074468/0 /scratch/stefan/7916156/working/building/REAL250005074468 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 590) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/590 `/scratch/stefan/7916156/working/3D/590' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)C(C)(C)O)C1CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074468.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074468/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074468 none C[C@H](NC(=O)C(C)(C)O)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 5, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [35, 21, 35, 35, 51, 51, 51, 72, 72, 72, 21, 21, 10, 1, 10, 1, 1, 1, 1, 1, 1, 21, 35, 35, 35, 51, 72, 72, 72, 72, 72, 72, 216, 21, 21, 21, 1, 21, 21] 216 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: 479 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074468 none C[C@H](NC(=O)C(C)(C)O)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 5, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 1, 6, 6, 15, 15, 15, 53, 53, 51, 1, 1, 1, 1, 6, 6, 21, 21, 21, 21, 21, 1, 6, 6, 6, 15, 53, 53, 53, 53, 53, 53, 159, 1, 1, 1, 21, 1, 1] 216 rigid atoms, others: [1, 34, 35, 37, 38, 33, 10, 11, 12, 13, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36]) total number of confs: 380 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074468 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074468 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074468/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074468 Building REAL250005074469 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074469' /scratch/stefan/7916156/working/building/REAL250005074469 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074469 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074469/0 /scratch/stefan/7916156/working/building/REAL250005074469 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 591) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/591 `/scratch/stefan/7916156/working/3D/591' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC1C(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074469.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074469/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074469 none CC1=CC1C(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [81, 81, 81, 17, 17, 17, 6, 1, 6, 6, 1, 1, 1, 1, 6, 6, 29, 29, 29, 29, 29, 1, 81, 81, 81, 81, 81, 17, 6, 6, 6, 1, 1, 1, 30, 1, 1] 142 rigid atoms, others: [32, 33, 35, 36, 7, 10, 11, 12, 13, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34]) total number of confs: 244 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074469 none CC1=CC1C(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 142 conformations in input total number of sets (complete confs): 142 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 13, 13, 13, 47, 47, 47, 81, 81, 81, 122, 122, 142, 142, 142, 142, 142, 81, 2, 2, 2, 1, 1, 13, 47, 47, 47, 81, 81, 81, 142, 81, 81] 142 rigid atoms, others: [0, 1, 2, 3, 4, 25, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 470 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.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: REAL250005074469 none CC1=CC1C(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 142 conformations in input total number of sets (complete confs): 142 using faster count positions algorithm for large data unique positions, atoms: [142, 142, 142, 80, 80, 80, 58, 30, 58, 58, 30, 30, 11, 1, 11, 1, 1, 1, 1, 1, 1, 29, 142, 142, 142, 142, 142, 80, 58, 58, 58, 30, 30, 30, 1, 29, 30] 142 rigid atoms, others: [34, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36]) total number of confs: 445 number of broken/clashed sets: 5 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074469 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074469 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074469/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074469 Building REAL250005074470 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074470' /scratch/stefan/7916156/working/building/REAL250005074470 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074470 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074470/0 /scratch/stefan/7916156/working/building/REAL250005074470 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 592) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/592 `/scratch/stefan/7916156/working/3D/592' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)C(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074470.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074470/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074470 none C[C@@H](O)C(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 168 conformations in input total number of sets (complete confs): 168 using faster count positions algorithm for large data unique positions, atoms: [56, 50, 56, 56, 50, 50, 34, 19, 34, 34, 19, 19, 9, 1, 9, 1, 1, 1, 1, 1, 1, 19, 56, 56, 56, 168, 50, 34, 34, 34, 19, 19, 19, 1, 19, 19] 168 rigid atoms, others: [33, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35]) total number of confs: 364 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074470 none C[C@@H](O)C(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 168 conformations in input total number of sets (complete confs): 168 using faster count positions algorithm for large data unique positions, atoms: [40, 15, 40, 40, 15, 15, 6, 1, 6, 6, 1, 1, 1, 1, 5, 5, 19, 19, 19, 19, 19, 1, 40, 40, 40, 120, 15, 6, 6, 6, 1, 1, 1, 19, 1, 1] 168 rigid atoms, others: [32, 34, 35, 7, 10, 11, 12, 13, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 33]) total number of confs: 298 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074470 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074470 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074470/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074470 Building REAL250005074471 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074471' /scratch/stefan/7916156/working/building/REAL250005074471 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074471 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074471/0 /scratch/stefan/7916156/working/building/REAL250005074471 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 593) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/593 `/scratch/stefan/7916156/working/3D/593' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)C=CCO)C1CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074471.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074471/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074471 none C[C@H](NC(=O)C=CCO)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 384 conformations in input total number of sets (complete confs): 384 using faster count positions algorithm for large data unique positions, atoms: [43, 19, 43, 43, 75, 75, 75, 124, 124, 128, 19, 19, 8, 1, 8, 1, 1, 1, 1, 1, 1, 19, 43, 43, 43, 75, 124, 124, 128, 128, 384, 19, 19, 19, 1, 19, 19] 384 rigid atoms, others: [34, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36]) total number of confs: 823 number of broken/clashed sets: 27 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074471 none C[C@H](NC(=O)C=CCO)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 384 conformations in input total number of sets (complete confs): 384 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 18, 18, 18, 62, 62, 105, 1, 1, 1, 1, 7, 7, 19, 19, 19, 19, 19, 1, 6, 6, 6, 18, 62, 62, 105, 105, 315, 1, 1, 1, 19, 1, 1] 384 rigid atoms, others: [32, 1, 35, 36, 33, 10, 11, 12, 13, 21, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34]) total number of confs: 727 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074471 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074471 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074471/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074471 Building REAL250005074472 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074472' /scratch/stefan/7916156/working/building/REAL250005074472 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074472 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074472/0 /scratch/stefan/7916156/working/building/REAL250005074472 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 594) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/594 `/scratch/stefan/7916156/working/3D/594' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)C1=CCC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074472.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074472.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074472/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074472 none C[C@H](NC(=O)C1=CCC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [6, 1, 6, 6, 12, 12, 12, 18, 18, 18, 1, 1, 1, 1, 7, 7, 18, 18, 18, 18, 18, 1, 6, 6, 6, 12, 18, 18, 18, 18, 18, 1, 1, 1, 18, 1, 1] 34 rigid atoms, others: [32, 1, 35, 36, 33, 10, 11, 12, 13, 21, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34]) total number of confs: 78 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074472 none C[C@H](NC(=O)C1=CCC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [11, 6, 11, 6, 1, 6, 1, 1, 1, 1, 11, 18, 18, 18, 29, 29, 34, 34, 34, 34, 34, 18, 11, 11, 11, 6, 1, 1, 1, 1, 1, 18, 18, 18, 34, 18, 18] 34 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, 33, 34, 35, 36]) total number of confs: 99 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.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: REAL250005074472 none C[C@H](NC(=O)C1=CCC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [29, 18, 29, 29, 34, 34, 34, 34, 34, 34, 18, 18, 8, 1, 8, 1, 1, 1, 1, 1, 1, 18, 29, 29, 29, 34, 34, 34, 34, 34, 34, 18, 18, 18, 1, 18, 18] 34 rigid atoms, others: [34, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36]) total number of confs: 101 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074472 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074472 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074472/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074472 Building REAL250005074473 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074473' /scratch/stefan/7916156/working/building/REAL250005074473 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074473 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074473/0 /scratch/stefan/7916156/working/building/REAL250005074473 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 595) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/595 `/scratch/stefan/7916156/working/3D/595' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CON=CC(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074473.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074473/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074473 none CON=CC(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 8, 1, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 51, 51, 51, 37, 23, 37, 37, 23, 23, 10, 1, 10, 1, 1, 1, 1, 1, 1, 23, 63, 63, 63, 63, 51, 37, 37, 37, 23, 23, 23, 1, 23, 23] 63 rigid atoms, others: [33, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35]) total number of confs: 194 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074473 none CON=CC(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 8, 1, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [41, 33, 33, 15, 15, 15, 6, 1, 6, 6, 1, 1, 1, 1, 7, 7, 23, 23, 23, 23, 23, 1, 41, 41, 41, 33, 15, 6, 6, 6, 1, 1, 1, 23, 1, 1] 63 rigid atoms, others: [32, 34, 35, 7, 10, 11, 12, 13, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 33]) total number of confs: 142 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074473 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074473 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074473/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074473 Building REAL250005074474 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074474' /scratch/stefan/7916156/working/building/REAL250005074474 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074474 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074474/0 /scratch/stefan/7916156/working/building/REAL250005074474 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 596) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/596 `/scratch/stefan/7916156/working/3D/596' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)C1(F)CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074474.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074474/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074474 none C[C@H](NC(=O)C1(F)CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 15, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 17, 17, 17, 61, 61, 61, 1, 1, 1, 1, 6, 6, 25, 25, 25, 25, 25, 1, 6, 6, 6, 17, 61, 61, 61, 61, 1, 1, 1, 26, 1, 1] 99 rigid atoms, others: [32, 1, 34, 35, 10, 11, 12, 13, 21, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 33]) total number of confs: 201 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074474 none C[C@H](NC(=O)C1(F)CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 15, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [38, 11, 38, 11, 1, 11, 1, 1, 1, 1, 38, 61, 61, 61, 88, 88, 99, 99, 99, 99, 99, 61, 38, 38, 38, 11, 1, 1, 1, 1, 61, 61, 61, 99, 61, 61] 99 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, 32, 33, 34, 35]) 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.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: REAL250005074474 none C[C@H](NC(=O)C1(F)CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 15, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [48, 26, 48, 48, 71, 71, 71, 99, 99, 99, 26, 26, 10, 1, 10, 1, 1, 1, 1, 1, 1, 25, 48, 48, 48, 71, 99, 99, 99, 99, 26, 26, 26, 1, 25, 26] 99 rigid atoms, others: [33, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35]) total number of confs: 332 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074474 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074474 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074474/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074474 Building REAL250005074475 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074475' /scratch/stefan/7916156/working/building/REAL250005074475 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074475 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074475/0 /scratch/stefan/7916156/working/building/REAL250005074475 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 597) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/597 `/scratch/stefan/7916156/working/3D/597' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=C(F)C(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074475.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074475.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074475/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074475 none CC=C(F)C(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 44, 52, 44, 44, 32, 20, 32, 32, 20, 20, 8, 1, 8, 1, 1, 1, 1, 1, 1, 20, 52, 52, 52, 52, 44, 32, 32, 32, 20, 20, 20, 1, 20, 20] 52 rigid atoms, others: [33, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35]) total number of confs: 168 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074475 none CC=C(F)C(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [30, 30, 13, 30, 13, 13, 6, 1, 6, 6, 1, 1, 1, 1, 7, 7, 20, 20, 20, 20, 20, 1, 30, 30, 30, 30, 13, 6, 6, 6, 1, 1, 1, 20, 1, 1] 52 rigid atoms, others: [32, 34, 35, 7, 10, 11, 12, 13, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 33]) total number of confs: 121 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074475 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074475 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074475/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074475 Building REAL250005074476 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074476' /scratch/stefan/7916156/working/building/REAL250005074476 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074476 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074476/0 /scratch/stefan/7916156/working/building/REAL250005074476 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 598) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/598 `/scratch/stefan/7916156/working/3D/598' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CO)C(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074476.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074476.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074476/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074476 none CC(CO)C(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 453 conformations in input total number of sets (complete confs): 453 using faster count positions algorithm for large data unique positions, atoms: [148, 79, 148, 151, 79, 79, 41, 20, 41, 41, 20, 20, 8, 1, 8, 1, 1, 1, 1, 1, 1, 20, 148, 148, 148, 148, 151, 151, 453, 79, 41, 41, 41, 20, 20, 20, 1, 20, 20] 453 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: 1044 number of broken/clashed sets: 59 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074476 none CC(CO)C(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 453 conformations in input total number of sets (complete confs): 453 using faster count positions algorithm for large data unique positions, atoms: [79, 16, 79, 115, 16, 16, 6, 1, 6, 6, 1, 1, 1, 1, 7, 7, 20, 20, 20, 20, 20, 1, 79, 79, 79, 79, 115, 115, 345, 16, 6, 6, 6, 1, 1, 1, 20, 1, 1] 453 rigid atoms, others: [33, 34, 35, 37, 38, 7, 10, 11, 12, 13, 21] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36]) total number of confs: 840 number of broken/clashed sets: 59 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074476 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074476 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074476/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074476 Building REAL250005074477 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074477' /scratch/stefan/7916156/working/building/REAL250005074477 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074477 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074477/0 /scratch/stefan/7916156/working/building/REAL250005074477 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 599) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/599 `/scratch/stefan/7916156/working/3D/599' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)C(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074477.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074477/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074477 none C[C@H](O)C(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 207 conformations in input total number of sets (complete confs): 207 using faster count positions algorithm for large data unique positions, atoms: [69, 57, 69, 69, 57, 57, 43, 24, 43, 43, 24, 24, 9, 1, 9, 1, 1, 1, 1, 1, 1, 24, 69, 69, 69, 207, 57, 43, 43, 43, 24, 24, 24, 1, 24, 24] 207 rigid atoms, others: [33, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35]) total number of confs: 453 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074477 none C[C@H](O)C(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 207 conformations in input total number of sets (complete confs): 207 using faster count positions algorithm for large data unique positions, atoms: [48, 14, 48, 48, 14, 14, 6, 1, 6, 6, 1, 1, 1, 1, 6, 6, 24, 24, 24, 24, 24, 1, 48, 48, 48, 144, 14, 6, 6, 6, 1, 1, 1, 24, 1, 1] 207 rigid atoms, others: [32, 34, 35, 7, 10, 11, 12, 13, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 33]) total number of confs: 358 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074477 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074477 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074477/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074477 Building REAL250005074478 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074478' /scratch/stefan/7916156/working/building/REAL250005074478 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074478 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074478/0 /scratch/stefan/7916156/working/building/REAL250005074478 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 600) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/600 `/scratch/stefan/7916156/working/3D/600' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C1CC1C(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074478.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074478/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074478 none C=C1CC1C(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 134 conformations in input total number of sets (complete confs): 134 using faster count positions algorithm for large data unique positions, atoms: [82, 82, 82, 15, 15, 15, 6, 1, 6, 6, 1, 1, 1, 1, 7, 7, 27, 27, 27, 27, 27, 1, 82, 82, 82, 82, 82, 15, 6, 6, 6, 1, 1, 1, 27, 1, 1] 134 rigid atoms, others: [32, 33, 35, 36, 7, 10, 11, 12, 13, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34]) total number of confs: 245 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074478 none C=C1CC1C(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 134 conformations in input total number of sets (complete confs): 134 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 13, 13, 13, 47, 47, 47, 82, 82, 82, 114, 114, 134, 134, 134, 134, 134, 82, 1, 1, 1, 1, 1, 13, 47, 47, 47, 82, 82, 82, 134, 82, 82] 134 rigid atoms, others: [0, 1, 2, 3, 4, 22, 23, 24, 25, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 433 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.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: REAL250005074478 none C=C1CC1C(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 134 conformations in input total number of sets (complete confs): 134 using faster count positions algorithm for large data unique positions, atoms: [134, 134, 134, 79, 79, 79, 52, 27, 52, 52, 27, 27, 10, 1, 10, 1, 1, 1, 1, 1, 1, 27, 134, 134, 134, 134, 134, 79, 52, 52, 52, 27, 27, 27, 1, 27, 27] 134 rigid atoms, others: [34, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36]) total number of confs: 419 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074478 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074478 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074478/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074478 Building REAL250005074479 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074479' /scratch/stefan/7916156/working/building/REAL250005074479 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074479 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074479/0 /scratch/stefan/7916156/working/building/REAL250005074479 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 601) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/601 `/scratch/stefan/7916156/working/3D/601' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CF)C(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074479.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074479/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074479 none CC(CF)C(=O)N[C@@H](C)C1CN(C(=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', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 7, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [194, 96, 194, 195, 96, 96, 47, 21, 47, 47, 21, 21, 8, 1, 8, 1, 1, 1, 1, 1, 1, 21, 194, 194, 194, 194, 195, 195, 96, 47, 47, 47, 21, 21, 21, 1, 21, 21] 195 rigid atoms, others: [35, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37]) total number of confs: 771 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074479 none CC(CF)C(=O)N[C@@H](C)C1CN(C(=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', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 7, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [91, 17, 91, 138, 17, 17, 6, 1, 6, 6, 1, 1, 1, 1, 7, 7, 21, 21, 21, 21, 21, 1, 91, 91, 91, 91, 138, 138, 17, 6, 6, 6, 1, 1, 1, 21, 1, 1] 195 rigid atoms, others: [32, 33, 34, 36, 37, 7, 10, 11, 12, 13, 21] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35]) total number of confs: 591 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074479 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074479 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074479/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074479 Building REAL250005074480 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074480' /scratch/stefan/7916156/working/building/REAL250005074480 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074480 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074480/0 /scratch/stefan/7916156/working/building/REAL250005074480 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 602) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/602 `/scratch/stefan/7916156/working/3D/602' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)CC(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074480.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074480.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074480/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074480 none C=C(C)CC(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 174 conformations in input total number of sets (complete confs): 174 using faster count positions algorithm for large data unique positions, atoms: [174, 174, 174, 88, 88, 88, 46, 27, 46, 46, 27, 27, 12, 1, 12, 1, 1, 1, 1, 1, 1, 27, 174, 174, 174, 174, 174, 174, 174, 88, 46, 46, 46, 27, 27, 27, 1, 27, 27] 174 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: 650 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074480 none C=C(C)CC(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [115, 92, 115, 17, 17, 17, 6, 1, 6, 6, 1, 1, 1, 1, 6, 6, 27, 27, 27, 27, 27, 1, 115, 115, 115, 115, 115, 92, 92, 17, 6, 6, 6, 1, 1, 1, 27, 1, 1] 174 rigid atoms, others: [33, 34, 35, 37, 38, 7, 10, 11, 12, 13, 21] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36]) total number of confs: 443 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074480 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074480 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074480/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074480 Building REAL250005074481 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074481' /scratch/stefan/7916156/working/building/REAL250005074481 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074481 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074481/0 /scratch/stefan/7916156/working/building/REAL250005074481 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 603) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/603 `/scratch/stefan/7916156/working/3D/603' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074481.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074481/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074481 none CC=CC(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [73, 73, 62, 62, 62, 45, 24, 45, 45, 24, 24, 10, 1, 10, 1, 1, 1, 1, 1, 1, 24, 73, 73, 73, 73, 73, 62, 45, 45, 45, 24, 24, 24, 1, 24, 24] 73 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: 239 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074481 none CC=CC(=O)N[C@@H](C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 43, 16, 16, 16, 6, 1, 6, 6, 1, 1, 1, 1, 7, 7, 24, 24, 24, 24, 24, 1, 43, 43, 43, 43, 43, 16, 6, 6, 6, 1, 1, 1, 24, 1, 1] 73 rigid atoms, others: [32, 34, 35, 6, 9, 10, 11, 12, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33]) total number of confs: 156 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074481 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074481 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074481/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074481 Building REAL250005074482 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074482' /scratch/stefan/7916156/working/building/REAL250005074482 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074482 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074482/0 /scratch/stefan/7916156/working/building/REAL250005074482 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 604) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/604 `/scratch/stefan/7916156/working/3D/604' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@H]1C[C@H]1C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074482.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074482/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074482 none C[C@H](NC(=O)[C@@H]1C[C@H]1C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 114 conformations in input total number of sets (complete confs): 114 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 15, 15, 15, 62, 62, 62, 62, 62, 1, 1, 1, 1, 6, 6, 26, 26, 27, 26, 26, 1, 6, 6, 6, 15, 62, 62, 62, 62, 62, 1, 1, 1, 27, 1, 1] 114 rigid atoms, others: [1, 34, 35, 37, 38, 33, 12, 13, 14, 15, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36]) total number of confs: 202 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074482 none C[C@H](NC(=O)[C@@H]1C[C@H]1C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 114 conformations in input total number of sets (complete confs): 114 using faster count positions algorithm for large data unique positions, atoms: [35, 13, 35, 13, 1, 13, 1, 1, 1, 1, 1, 1, 35, 62, 62, 62, 96, 96, 114, 114, 114, 114, 114, 62, 35, 35, 35, 13, 1, 1, 2, 2, 2, 62, 62, 62, 114, 62, 62] 114 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, 35, 36, 37, 38]) total number of confs: 368 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.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: REAL250005074482 none C[C@H](NC(=O)[C@@H]1C[C@H]1C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 114 conformations in input total number of sets (complete confs): 114 using faster count positions algorithm for large data unique positions, atoms: [46, 27, 46, 46, 64, 64, 64, 114, 114, 114, 114, 114, 27, 27, 9, 1, 9, 1, 1, 1, 1, 1, 1, 26, 46, 46, 46, 64, 114, 114, 114, 114, 114, 27, 27, 27, 1, 26, 27] 114 rigid atoms, others: [36, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 364 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074482 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074482 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074482/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074482 Building REAL250005074483 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074483' /scratch/stefan/7916156/working/building/REAL250005074483 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074483 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074483/0 /scratch/stefan/7916156/working/building/REAL250005074483 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 605) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/605 `/scratch/stefan/7916156/working/3D/605' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)C1(O)CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074483.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074483.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074483/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074483 none C[C@H](NC(=O)C1(O)CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 258 conformations in input total number of sets (complete confs): 258 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 15, 15, 15, 59, 59, 59, 1, 1, 1, 1, 6, 6, 22, 22, 22, 22, 22, 1, 6, 6, 6, 15, 177, 59, 59, 59, 59, 1, 1, 1, 22, 1, 1] 258 rigid atoms, others: [32, 1, 35, 36, 33, 10, 11, 12, 13, 21, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34]) total number of confs: 368 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074483 none C[C@H](NC(=O)C1(O)CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 258 conformations in input total number of sets (complete confs): 258 using faster count positions algorithm for large data unique positions, atoms: [34, 12, 34, 12, 1, 12, 1, 1, 1, 1, 34, 59, 59, 59, 77, 77, 86, 86, 86, 86, 86, 59, 34, 34, 34, 12, 6, 1, 1, 1, 1, 59, 59, 59, 86, 59, 59] 258 rigid atoms, others: [4, 6, 7, 8, 9, 27, 28, 29, 30] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36]) 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.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: REAL250005074483 none C[C@H](NC(=O)C1(O)CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 258 conformations in input total number of sets (complete confs): 258 using faster count positions algorithm for large data unique positions, atoms: [42, 23, 42, 42, 64, 64, 64, 86, 86, 86, 23, 23, 9, 1, 9, 1, 1, 1, 1, 1, 1, 22, 42, 42, 42, 64, 258, 86, 86, 86, 86, 23, 23, 23, 1, 22, 22] 258 rigid atoms, others: [34, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36]) total number of confs: 552 number of broken/clashed sets: 6 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074483 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074483 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074483/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074483 Building REAL250005074484 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074484' /scratch/stefan/7916156/working/building/REAL250005074484 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074484 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074484/0 /scratch/stefan/7916156/working/building/REAL250005074484 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 606) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/606 `/scratch/stefan/7916156/working/3D/606' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)CC2CC2)C1) `REAL250005074484.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074484/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074484 none C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)CC2CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 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 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 19, 19, 19, 41, 41, 41, 41, 41, 1, 1, 1, 1, 6, 6, 31, 53, 53, 1, 6, 6, 6, 19, 41, 1, 1, 1, 31, 31, 53, 53, 53, 53, 53, 1, 1] 125 rigid atoms, others: [1, 37, 38, 12, 13, 14, 15, 21, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 277 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074484 none C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)CC2CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 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 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [24, 7, 24, 7, 1, 7, 1, 1, 1, 1, 1, 1, 24, 41, 41, 41, 64, 64, 105, 125, 125, 41, 24, 24, 24, 7, 1, 41, 41, 41, 105, 105, 125, 125, 125, 125, 125, 41, 41] 125 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, 37, 38]) total number of confs: 522 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.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: REAL250005074484 none C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)CC2CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 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 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [90, 53, 90, 90, 117, 117, 117, 125, 125, 125, 125, 125, 53, 53, 18, 3, 18, 1, 1, 1, 1, 53, 90, 90, 90, 117, 125, 53, 53, 53, 3, 3, 1, 1, 1, 1, 1, 53, 53] 125 rigid atoms, others: [32, 33, 34, 35, 36, 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, 37, 38]) total number of confs: 391 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074484 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074484 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074484/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074484 Building REAL250005074485 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074485' /scratch/stefan/7916156/working/building/REAL250005074485 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074485 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074485/0 /scratch/stefan/7916156/working/building/REAL250005074485 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 607) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/607 `/scratch/stefan/7916156/working/3D/607' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C(C)(C)F)C1) `REAL250005074485.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074485/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074485 none C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C(C)(C)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 5, 15, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 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 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 15, 15, 15, 22, 22, 22, 22, 22, 1, 1, 1, 1, 3, 3, 10, 10, 10, 1, 6, 6, 6, 15, 22, 1, 1, 1, 11, 11, 11, 11, 11, 11, 1, 1] 39 rigid atoms, others: [1, 36, 37, 12, 13, 14, 15, 21, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35]) total number of confs: 107 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074485 none C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C(C)(C)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 5, 15, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 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 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 13, 6, 1, 6, 1, 1, 1, 1, 1, 1, 13, 22, 22, 22, 31, 31, 39, 39, 39, 22, 13, 13, 13, 6, 1, 22, 22, 22, 39, 39, 39, 39, 39, 39, 22, 22] 39 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, 37]) total number of confs: 148 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074485 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074485 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074485/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074485 Building REAL250005074486 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074486' /scratch/stefan/7916156/working/building/REAL250005074486 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074486 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074486/0 /scratch/stefan/7916156/working/building/REAL250005074486 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 608) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/608 `/scratch/stefan/7916156/working/3D/608' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)N1CC([C@H](C)NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074486.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074486.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074486/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074486 none COCC(=O)N1CC([C@H](C)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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 7, 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, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 127 conformations in input total number of sets (complete confs): 127 using faster count positions algorithm for large data unique positions, atoms: [127, 124, 73, 46, 73, 46, 46, 24, 7, 24, 24, 7, 1, 7, 1, 1, 1, 1, 1, 1, 46, 127, 127, 127, 124, 124, 46, 46, 46, 24, 24, 24, 7, 1, 46, 46] 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, 34, 35]) total number of confs: 492 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074486 none COCC(=O)N1CC([C@H](C)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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 7, 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, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 127 conformations in input total number of sets (complete confs): 127 using faster count positions algorithm for large data unique positions, atoms: [69, 30, 6, 1, 6, 1, 1, 1, 1, 6, 6, 6, 20, 20, 20, 46, 46, 46, 46, 46, 1, 69, 69, 69, 30, 30, 1, 1, 1, 6, 6, 6, 20, 46, 1, 1] 127 rigid atoms, others: [34, 3, 5, 6, 7, 8, 35, 20, 26, 27, 28] set([0, 1, 2, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33]) total number of confs: 250 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074486 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074486 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074486/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074486 Building REAL250005074487 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074487' /scratch/stefan/7916156/working/building/REAL250005074487 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074487 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074487/0 /scratch/stefan/7916156/working/building/REAL250005074487 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 609) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/609 `/scratch/stefan/7916156/working/3D/609' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)N1CC([C@H](C)NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074487.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074487/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074487 none CCCC(=O)N1CC([C@H](C)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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 7, 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, 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 130 conformations in input total number of sets (complete confs): 130 using faster count positions algorithm for large data unique positions, atoms: [130, 123, 79, 48, 79, 48, 48, 23, 8, 23, 23, 8, 1, 8, 1, 1, 1, 1, 1, 1, 48, 130, 130, 130, 130, 130, 123, 123, 48, 48, 48, 23, 23, 23, 8, 1, 48, 48] 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, 36, 37]) total number of confs: 518 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074487 none CCCC(=O)N1CC([C@H](C)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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 7, 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, 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 130 conformations in input total number of sets (complete confs): 130 using faster count positions algorithm for large data unique positions, atoms: [41, 30, 6, 1, 6, 1, 1, 1, 1, 6, 6, 6, 19, 19, 19, 48, 48, 48, 48, 48, 1, 48, 48, 48, 47, 47, 30, 30, 1, 1, 1, 6, 6, 6, 19, 48, 1, 1] 130 rigid atoms, others: [3, 36, 5, 6, 7, 8, 20, 28, 29, 30, 37] set([0, 1, 2, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35]) total number of confs: 323 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074487 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074487 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074487/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074487 Building REAL250005074488 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074488' /scratch/stefan/7916156/working/building/REAL250005074488 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074488 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074488/0 /scratch/stefan/7916156/working/building/REAL250005074488 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 610) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/610 `/scratch/stefan/7916156/working/3D/610' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(=O)N1CC([C@H](C)NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074488.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074488/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074488 none CC(C)CC(=O)N1CC([C@H](C)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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [73, 70, 73, 43, 30, 43, 30, 30, 17, 6, 17, 17, 6, 1, 6, 1, 1, 1, 1, 1, 1, 30, 73, 73, 73, 73, 73, 73, 73, 70, 70, 30, 30, 30, 17, 17, 17, 6, 1, 30, 30] 73 rigid atoms, others: [38, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40]) total number of confs: 308 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074488 none CC(C)CC(=O)N1CC([C@H](C)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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [26, 24, 30, 6, 1, 6, 1, 1, 1, 1, 6, 6, 6, 16, 16, 16, 30, 30, 30, 30, 30, 1, 30, 30, 30, 30, 30, 30, 30, 24, 24, 1, 1, 1, 6, 6, 6, 16, 30, 1, 1] 73 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 39, 40, 21, 31] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38]) total number of confs: 213 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074488 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074488 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074488/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074488 Building REAL250005074489 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074489' /scratch/stefan/7916156/working/building/REAL250005074489 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074489 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074489/0 /scratch/stefan/7916156/working/building/REAL250005074489 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 611) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/611 `/scratch/stefan/7916156/working/3D/611' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2CC2C)C1) `REAL250005074489.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074489/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074489 none C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2CC2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 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 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 14, 14, 14, 25, 25, 25, 25, 25, 1, 1, 1, 1, 5, 5, 18, 18, 18, 1, 6, 6, 6, 14, 25, 1, 1, 1, 18, 18, 18, 18, 18, 18, 18, 1, 1] 53 rigid atoms, others: [1, 37, 38, 12, 13, 14, 15, 21, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 104 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074489 none C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2CC2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 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 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [17, 6, 17, 6, 1, 6, 1, 1, 1, 1, 1, 1, 17, 25, 25, 25, 34, 34, 53, 53, 53, 25, 17, 17, 17, 6, 1, 25, 25, 25, 53, 53, 53, 53, 53, 53, 53, 25, 25] 53 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, 37, 38]) total number of confs: 181 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.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: REAL250005074489 none C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2CC2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 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 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [36, 18, 36, 36, 49, 49, 49, 53, 53, 53, 53, 53, 18, 18, 8, 1, 8, 1, 1, 1, 1, 18, 36, 36, 36, 49, 53, 18, 18, 18, 1, 1, 1, 1, 2, 2, 2, 18, 18] 53 rigid atoms, others: [32, 33, 15, 17, 18, 19, 20, 30, 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, 34, 35, 36, 37, 38]) total number of confs: 172 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074489 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074489 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074489/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074489 Building REAL250005074490 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074490' /scratch/stefan/7916156/working/building/REAL250005074490 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074490 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074490/0 /scratch/stefan/7916156/working/building/REAL250005074490 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 612) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/612 `/scratch/stefan/7916156/working/3D/612' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCC(=O)N1CC([C@H](C)NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074490.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074490/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074490 none CCOCC(=O)N1CC([C@H](C)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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 12, 5, 1, 11, 8, 5, 5, 5, 7, 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, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 200, 174, 64, 36, 64, 36, 36, 17, 5, 17, 17, 5, 1, 5, 1, 1, 1, 1, 1, 1, 36, 201, 201, 201, 201, 201, 174, 174, 36, 36, 36, 17, 17, 17, 5, 1, 36, 36] 201 rigid atoms, others: [36, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 723 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074490 none CCOCC(=O)N1CC([C@H](C)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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 12, 5, 1, 11, 8, 5, 5, 5, 7, 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, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [123, 105, 38, 6, 1, 6, 1, 1, 1, 1, 6, 6, 6, 18, 18, 18, 36, 36, 36, 36, 36, 1, 124, 124, 124, 123, 123, 38, 38, 1, 1, 1, 6, 6, 6, 18, 36, 1, 1] 201 rigid atoms, others: [4, 37, 6, 7, 8, 9, 21, 38, 29, 30, 31] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36]) total number of confs: 413 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074490 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074490 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074490/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074490 Building REAL250005074491 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074491' /scratch/stefan/7916156/working/building/REAL250005074491 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074491 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074491/0 /scratch/stefan/7916156/working/building/REAL250005074491 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 613) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/613 `/scratch/stefan/7916156/working/3D/613' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)=CC(=O)N1CC([C@H](C)NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074491.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074491/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074491 none CC(C)=CC(=O)N1CC([C@H](C)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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 5, 1, 1, 11, 8, 5, 5, 5, 7, 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, 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 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 42, 30, 42, 30, 30, 15, 6, 15, 15, 6, 1, 6, 1, 1, 1, 1, 1, 1, 30, 63, 63, 63, 63, 63, 63, 63, 30, 30, 30, 15, 15, 15, 7, 1, 30, 30] 63 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: 225 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074491 none CC(C)=CC(=O)N1CC([C@H](C)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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 5, 1, 1, 11, 8, 5, 5, 5, 7, 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, 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 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 23, 6, 1, 6, 1, 1, 1, 1, 6, 6, 6, 16, 16, 16, 30, 30, 30, 30, 30, 1, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 6, 6, 6, 16, 30, 1, 1] 63 rigid atoms, others: [4, 37, 6, 7, 8, 9, 21, 38, 29, 30, 31] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36]) total number of confs: 127 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074491 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074491 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074491/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074491 Building REAL250005074492 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074492' /scratch/stefan/7916156/working/building/REAL250005074492 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074492 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074492/0 /scratch/stefan/7916156/working/building/REAL250005074492 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 614) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/614 `/scratch/stefan/7916156/working/3D/614' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSCC(=O)N1CC([C@H](C)NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074492.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074492/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074492 none CSCC(=O)N1CC([C@H](C)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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 14, 5, 1, 11, 8, 5, 5, 5, 7, 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, 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 155 conformations in input total number of sets (complete confs): 155 using faster count positions algorithm for large data unique positions, atoms: [155, 133, 73, 46, 73, 46, 46, 24, 8, 24, 24, 8, 1, 8, 1, 1, 1, 1, 1, 1, 46, 155, 155, 155, 133, 133, 46, 46, 46, 24, 24, 24, 8, 1, 46, 46] 155 rigid atoms, others: [33, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35]) total number of confs: 578 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074492 none CSCC(=O)N1CC([C@H](C)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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 14, 5, 1, 11, 8, 5, 5, 5, 7, 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, 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 155 conformations in input total number of sets (complete confs): 155 using faster count positions algorithm for large data unique positions, atoms: [74, 32, 5, 1, 5, 1, 1, 1, 1, 6, 6, 6, 20, 20, 20, 46, 46, 46, 46, 46, 1, 75, 75, 75, 32, 32, 1, 1, 1, 6, 6, 6, 20, 46, 1, 1] 155 rigid atoms, others: [34, 3, 5, 6, 7, 8, 35, 20, 26, 27, 28] set([0, 1, 2, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33]) total number of confs: 271 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074492 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074492 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074492/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074492 Building REAL250005074493 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074493' /scratch/stefan/7916156/working/building/REAL250005074493 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074493 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074493/0 /scratch/stefan/7916156/working/building/REAL250005074493 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 615) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/615 `/scratch/stefan/7916156/working/3D/615' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC(=O)N1CC([C@H](C)NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074493.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074493/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074493 none CCCCC(=O)N1CC([C@H](C)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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 188, 172, 77, 37, 77, 37, 37, 18, 6, 18, 18, 6, 1, 6, 1, 1, 1, 1, 1, 1, 37, 201, 201, 201, 201, 201, 188, 188, 172, 172, 37, 37, 37, 18, 18, 18, 6, 1, 37, 37] 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, 39, 40]) total number of confs: 844 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074493 none CCCCC(=O)N1CC([C@H](C)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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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: [86, 52, 35, 6, 1, 6, 1, 1, 1, 1, 6, 6, 6, 17, 17, 17, 37, 37, 37, 37, 37, 1, 86, 90, 90, 86, 85, 59, 59, 35, 35, 1, 1, 1, 6, 6, 6, 17, 37, 1, 1] 201 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 39, 40, 21, 31] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38]) total number of confs: 499 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074493 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074493 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074493/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074493 Building REAL250005074494 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074494' /scratch/stefan/7916156/working/building/REAL250005074494 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074494 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074494/0 /scratch/stefan/7916156/working/building/REAL250005074494 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 616) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/616 `/scratch/stefan/7916156/working/3D/616' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N1CC([C@H](C)NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074494.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074494/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074494 none CC(C)C(=O)N1CC([C@H](C)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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 7, 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, 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 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, 27, 35, 27, 27, 17, 7, 17, 17, 7, 1, 7, 1, 1, 1, 1, 1, 1, 27, 39, 39, 39, 39, 39, 39, 39, 27, 27, 27, 17, 17, 17, 8, 1, 27, 27] 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, 36, 37]) total number of confs: 143 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074494 none CC(C)C(=O)N1CC([C@H](C)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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 7, 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, 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 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 12, 1, 6, 1, 1, 1, 1, 6, 6, 6, 17, 17, 17, 27, 27, 27, 27, 27, 1, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 6, 6, 6, 17, 27, 1, 1] 39 rigid atoms, others: [3, 36, 5, 6, 7, 8, 20, 28, 29, 30, 37] set([0, 1, 2, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35]) total number of confs: 103 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074494 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074494 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074494/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074494 Building REAL250005074495 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074495' /scratch/stefan/7916156/working/building/REAL250005074495 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074495 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074495/0 /scratch/stefan/7916156/working/building/REAL250005074495 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 617) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/617 `/scratch/stefan/7916156/working/3D/617' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)C(=O)N1CC([C@H](C)NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074495.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074495/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074495 none CCC(C)C(=O)N1CC([C@H](C)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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 45, 63, 28, 45, 28, 28, 16, 6, 16, 16, 6, 1, 6, 1, 1, 1, 1, 1, 1, 28, 63, 63, 63, 63, 63, 63, 63, 63, 63, 28, 28, 28, 16, 16, 16, 6, 1, 28, 28] 63 rigid atoms, others: [38, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40]) total number of confs: 236 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074495 none CCC(C)C(=O)N1CC([C@H](C)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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [23, 19, 6, 19, 1, 6, 1, 1, 1, 1, 6, 6, 6, 17, 17, 17, 28, 28, 28, 28, 28, 1, 25, 25, 25, 25, 25, 19, 19, 19, 19, 1, 1, 1, 6, 6, 6, 17, 28, 1, 1] 63 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 39, 40, 21, 31] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38]) total number of confs: 177 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074495 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074495 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074495/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074495 Building REAL250005074496 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074496' /scratch/stefan/7916156/working/building/REAL250005074496 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074496 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074496/0 /scratch/stefan/7916156/working/building/REAL250005074496 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 618) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/618 `/scratch/stefan/7916156/working/3D/618' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)C(=O)N1CC([C@H](C)NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074496.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074496/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074496 none COC(C)C(=O)N1CC([C@H](C)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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 7, 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, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [84, 81, 56, 81, 38, 56, 38, 38, 20, 7, 20, 20, 7, 1, 7, 1, 1, 1, 1, 1, 1, 38, 84, 84, 84, 81, 81, 81, 81, 38, 38, 38, 20, 20, 20, 7, 1, 38, 38] 84 rigid atoms, others: [36, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 311 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074496 none COC(C)C(=O)N1CC([C@H](C)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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 7, 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, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [41, 28, 6, 28, 1, 6, 1, 1, 1, 1, 6, 6, 6, 19, 19, 19, 38, 38, 38, 38, 38, 1, 41, 41, 41, 28, 28, 28, 28, 1, 1, 1, 6, 6, 6, 19, 38, 1, 1] 84 rigid atoms, others: [4, 37, 6, 7, 8, 9, 21, 38, 29, 30, 31] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36]) total number of confs: 201 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074496 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074496 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074496/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074496 Building REAL250005074497 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074497' /scratch/stefan/7916156/working/building/REAL250005074497 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074497 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074497/0 /scratch/stefan/7916156/working/building/REAL250005074497 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 619) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/619 `/scratch/stefan/7916156/working/3D/619' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCC(=O)N1CC([C@H](C)NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074497.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074497/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074497 none C=CCCC(=O)N1CC([C@H](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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 7, 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, 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: [201, 201, 174, 77, 38, 77, 38, 38, 19, 6, 19, 19, 6, 1, 6, 1, 1, 1, 1, 1, 1, 38, 201, 201, 201, 201, 201, 174, 174, 38, 38, 38, 19, 19, 19, 6, 1, 38, 38] 201 rigid atoms, others: [36, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 835 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074497 none C=CCCC(=O)N1CC([C@H](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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 7, 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, 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: [114, 62, 33, 6, 1, 6, 1, 1, 1, 1, 6, 6, 6, 18, 18, 18, 38, 38, 38, 38, 38, 1, 114, 114, 114, 62, 62, 33, 33, 1, 1, 1, 6, 6, 6, 18, 38, 1, 1] 201 rigid atoms, others: [4, 37, 6, 7, 8, 9, 21, 38, 29, 30, 31] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36]) total number of confs: 516 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074497 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074497 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074497/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074497 Building REAL250005074498 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074498' /scratch/stefan/7916156/working/building/REAL250005074498 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074498 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074498/0 /scratch/stefan/7916156/working/building/REAL250005074498 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 620) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/620 `/scratch/stefan/7916156/working/3D/620' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C#N)C(=O)N1CC([C@H](C)NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074498.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074498/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074498 none CC(C#N)C(=O)N1CC([C@H](C)NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.1', 'N.1', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 8, 1, 11, 8, 5, 5, 5, 7, 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, 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 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [61, 44, 61, 61, 30, 44, 30, 30, 18, 7, 18, 18, 7, 1, 7, 1, 1, 1, 1, 1, 1, 30, 61, 61, 61, 61, 30, 30, 30, 18, 18, 18, 8, 1, 30, 30] 61 rigid atoms, others: [33, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35]) total number of confs: 239 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074498 none CC(C#N)C(=O)N1CC([C@H](C)NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.1', 'N.1', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 8, 1, 11, 8, 5, 5, 5, 7, 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, 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 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [24, 7, 24, 24, 1, 7, 1, 1, 1, 1, 6, 6, 6, 17, 17, 17, 30, 30, 30, 30, 30, 1, 24, 24, 24, 24, 1, 1, 1, 6, 6, 6, 17, 30, 1, 1] 61 rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 21, 26, 27, 28] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 29, 30, 31, 32, 33]) total number of confs: 152 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074498 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074498 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074498/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074498 Building REAL250005074499 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074499' /scratch/stefan/7916156/working/building/REAL250005074499 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074499 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074499/0 /scratch/stefan/7916156/working/building/REAL250005074499 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 621) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/621 `/scratch/stefan/7916156/working/3D/621' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=C(C)C(=O)N1CC([C@H](C)NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074499.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074499/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074499 none CC=C(C)C(=O)N1CC([C@H](C)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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 1, 5, 1, 11, 8, 5, 5, 5, 7, 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, 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 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [61, 61, 40, 61, 24, 40, 24, 24, 13, 5, 13, 13, 5, 1, 5, 1, 1, 1, 1, 1, 1, 24, 61, 61, 61, 61, 61, 61, 61, 24, 24, 24, 13, 13, 13, 5, 1, 24, 24] 61 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: 216 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074499 none CC=C(C)C(=O)N1CC([C@H](C)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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 1, 5, 1, 11, 8, 5, 5, 5, 7, 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, 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 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 6, 20, 1, 6, 1, 1, 1, 1, 5, 5, 5, 16, 16, 16, 24, 24, 24, 24, 24, 1, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 5, 5, 5, 16, 24, 1, 1] 61 rigid atoms, others: [4, 37, 6, 7, 8, 9, 21, 38, 29, 30, 31] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36]) total number of confs: 113 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074499 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074499 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074499/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074499 Building REAL250005074500 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074500' /scratch/stefan/7916156/working/building/REAL250005074500 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074500 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074500/0 /scratch/stefan/7916156/working/building/REAL250005074500 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 622) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/622 `/scratch/stefan/7916156/working/3D/622' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N1CC([C@H](C)NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074500.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074500.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074500/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074500 none CCC(=O)N1CC([C@H](C)NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 7, 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, 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 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [49, 38, 30, 38, 30, 30, 18, 8, 18, 18, 8, 1, 8, 1, 1, 1, 1, 1, 1, 30, 49, 49, 49, 49, 49, 30, 30, 30, 18, 18, 18, 8, 1, 30, 30] 49 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: 197 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074500 none CCC(=O)N1CC([C@H](C)NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 7, 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, 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 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [10, 4, 1, 3, 1, 1, 1, 1, 6, 6, 6, 17, 17, 17, 30, 30, 30, 30, 30, 1, 10, 9, 9, 10, 10, 1, 1, 1, 6, 6, 6, 17, 30, 1, 1] 49 rigid atoms, others: [33, 2, 4, 5, 6, 7, 34, 19, 25, 26, 27] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32]) total number of confs: 105 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074500 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074500 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074500/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074500 Building REAL250005074501 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074501' /scratch/stefan/7916156/working/building/REAL250005074501 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074501 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074501/0 /scratch/stefan/7916156/working/building/REAL250005074501 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 623) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/623 `/scratch/stefan/7916156/working/3D/623' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC(=O)N1CC([C@H](C)NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074501.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074501/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074501 none COCCC(=O)N1CC([C@H](C)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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 7, 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, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 199, 170, 77, 42, 77, 42, 42, 19, 6, 19, 19, 6, 1, 6, 1, 1, 1, 1, 1, 1, 42, 201, 201, 201, 199, 199, 170, 170, 42, 42, 42, 19, 19, 19, 6, 1, 42, 42] 201 rigid atoms, others: [36, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 830 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074501 none COCCC(=O)N1CC([C@H](C)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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 7, 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, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [111, 60, 36, 6, 1, 6, 1, 1, 1, 1, 6, 6, 6, 20, 20, 20, 42, 42, 42, 42, 42, 1, 112, 112, 112, 60, 60, 36, 36, 1, 1, 1, 6, 6, 6, 20, 42, 1, 1] 201 rigid atoms, others: [4, 37, 6, 7, 8, 9, 21, 38, 29, 30, 31] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36]) total number of confs: 416 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074501 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074501 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074501/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074501 Building REAL250005074502 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074502' /scratch/stefan/7916156/working/building/REAL250005074502 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074502 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074502/0 /scratch/stefan/7916156/working/building/REAL250005074502 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 624) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/624 `/scratch/stefan/7916156/working/3D/624' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC([C@H](C)NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074502.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074502/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074502 none CC(=O)N1CC([C@H](C)NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 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 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [20, 14, 20, 14, 14, 11, 5, 11, 11, 5, 1, 5, 1, 1, 1, 1, 1, 1, 14, 20, 20, 20, 14, 14, 14, 11, 11, 11, 5, 1, 14, 14] 20 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]) total number of confs: 72 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074502 none CC(=O)N1CC([C@H](C)NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 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 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 6, 6, 6, 11, 11, 11, 14, 14, 14, 14, 14, 1, 3, 3, 3, 1, 1, 1, 6, 6, 6, 11, 14, 1, 1] 20 rigid atoms, others: [1, 3, 4, 5, 6, 18, 22, 23, 24, 30, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 25, 26, 27, 28, 29]) total number of confs: 48 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074502 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074502 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074502/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074502 Building REAL250005074503 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074503' /scratch/stefan/7916156/working/building/REAL250005074503 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074503 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074503/0 /scratch/stefan/7916156/working/building/REAL250005074503 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 625) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/625 `/scratch/stefan/7916156/working/3D/625' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2CC2)C1) `REAL250005074503.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074503/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074503 none C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 19, 19, 19, 35, 35, 35, 35, 35, 1, 1, 1, 1, 3, 3, 17, 17, 1, 6, 6, 6, 19, 35, 1, 1, 1, 17, 17, 17, 17, 17, 1, 1] 54 rigid atoms, others: [1, 34, 35, 12, 13, 14, 15, 20, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33]) total number of confs: 117 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074503 none C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [19, 7, 19, 6, 1, 6, 1, 1, 1, 1, 1, 1, 19, 35, 35, 35, 38, 38, 54, 54, 35, 19, 19, 19, 7, 1, 35, 35, 35, 54, 54, 54, 54, 54, 35, 35] 54 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, 32, 33, 34, 35]) total number of confs: 194 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.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: REAL250005074503 none C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [36, 17, 36, 36, 49, 49, 49, 54, 54, 54, 54, 54, 17, 17, 8, 1, 8, 1, 1, 1, 17, 36, 36, 36, 49, 54, 17, 17, 17, 1, 1, 1, 1, 1, 17, 17] 54 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, 34, 35]) total number of confs: 180 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074503 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074503 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074503/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074503 Building REAL250005074504 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074504' /scratch/stefan/7916156/working/building/REAL250005074504 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074504 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074504/0 /scratch/stefan/7916156/working/building/REAL250005074504 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 626) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/626 `/scratch/stefan/7916156/working/3D/626' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2CCC2)C1) `REAL250005074504.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074504.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074504/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074504 none C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 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 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 17, 17, 17, 38, 38, 38, 38, 38, 1, 1, 1, 1, 5, 5, 16, 16, 16, 1, 5, 5, 5, 17, 38, 1, 1, 1, 16, 16, 16, 16, 16, 16, 16, 1, 1] 60 rigid atoms, others: [1, 37, 38, 12, 13, 14, 15, 21, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 121 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074504 none C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 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 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [24, 7, 24, 7, 1, 7, 1, 1, 1, 1, 1, 1, 24, 38, 38, 38, 49, 49, 60, 60, 60, 38, 24, 24, 24, 7, 1, 38, 38, 38, 60, 60, 60, 60, 60, 60, 60, 38, 38] 60 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, 37, 38]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.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: REAL250005074504 none C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 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 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [35, 16, 35, 35, 56, 56, 56, 60, 60, 60, 60, 60, 16, 16, 8, 1, 8, 1, 1, 1, 1, 16, 35, 35, 35, 56, 60, 16, 16, 16, 1, 1, 1, 1, 1, 1, 1, 16, 16] 60 rigid atoms, others: [32, 33, 34, 35, 36, 15, 17, 18, 19, 20, 30, 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, 37, 38]) total number of confs: 193 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074504 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074504 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074504/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074504 Building REAL250005074505 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074505' /scratch/stefan/7916156/working/building/REAL250005074505 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074505 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074505/0 /scratch/stefan/7916156/working/building/REAL250005074505 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 627) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/627 `/scratch/stefan/7916156/working/3D/627' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C(N)=O)C1) `REAL250005074505.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074505/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074505 none C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 1, 8, 11, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 15, 15, 15, 22, 22, 22, 22, 22, 1, 1, 1, 1, 4, 4, 18, 18, 1, 6, 6, 6, 15, 22, 1, 1, 1, 19, 19, 1, 1] 38 rigid atoms, others: [32, 1, 12, 13, 14, 15, 20, 26, 27, 28, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 21, 22, 23, 24, 25, 29, 30]) total number of confs: 103 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074505 none C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 1, 8, 11, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 4, 6, 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: [14, 5, 14, 5, 1, 5, 1, 1, 1, 1, 1, 1, 14, 22, 22, 22, 33, 33, 38, 38, 22, 14, 14, 14, 6, 1, 22, 22, 22, 38, 38, 22, 22] 38 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, 32]) total number of confs: 138 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074505 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074505 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074505/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074505 Building REAL250005074506 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074506' /scratch/stefan/7916156/working/building/REAL250005074506 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074506 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074506/0 /scratch/stefan/7916156/working/building/REAL250005074506 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 628) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/628 `/scratch/stefan/7916156/working/3D/628' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C(C)(C)C)C1) `REAL250005074506.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074506.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074506/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074506 none C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 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 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 15, 15, 15, 24, 24, 24, 24, 24, 1, 1, 1, 1, 6, 6, 8, 8, 8, 1, 6, 6, 6, 15, 24, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1] 30 rigid atoms, others: [1, 39, 40, 12, 13, 14, 15, 21, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 81 number of broken/clashed sets: 28 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074506 none C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 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 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 14, 6, 1, 6, 1, 1, 1, 1, 1, 1, 14, 24, 24, 24, 29, 29, 30, 30, 30, 24, 14, 14, 14, 7, 1, 24, 24, 24, 30, 30, 30, 30, 30, 30, 30, 30, 30, 24, 24] 30 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, 37, 38, 39, 40]) total number of confs: 109 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074506 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074506 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074506/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074506 Building REAL250005074507 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074507' /scratch/stefan/7916156/working/building/REAL250005074507 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074507 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074507/0 /scratch/stefan/7916156/working/building/REAL250005074507 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 629) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/629 `/scratch/stefan/7916156/working/3D/629' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2(C)CC2)C1) `REAL250005074507.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074507/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074507 none C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2(C)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 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 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 13, 13, 13, 18, 18, 18, 18, 18, 1, 1, 1, 1, 5, 5, 11, 11, 11, 1, 5, 5, 5, 13, 18, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 1, 1] 43 rigid atoms, others: [1, 37, 38, 12, 13, 14, 15, 21, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 80 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074507 none C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2(C)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 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 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 12, 5, 1, 5, 1, 1, 1, 1, 1, 1, 12, 18, 18, 18, 23, 23, 43, 43, 43, 18, 12, 12, 12, 5, 1, 18, 18, 18, 43, 43, 43, 43, 43, 43, 43, 18, 18] 43 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, 37, 38]) total number of confs: 156 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.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: REAL250005074507 none C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2(C)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 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 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [24, 11, 24, 24, 40, 40, 40, 43, 43, 43, 43, 43, 11, 11, 4, 1, 4, 1, 1, 1, 1, 11, 24, 24, 24, 40, 43, 11, 11, 11, 2, 2, 2, 1, 1, 1, 1, 11, 11] 43 rigid atoms, others: [33, 34, 35, 36, 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, 37, 38]) total number of confs: 143 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074507 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074507 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074507/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074507 Building REAL250005074508 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074508' /scratch/stefan/7916156/working/building/REAL250005074508 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074508 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074508/0 /scratch/stefan/7916156/working/building/REAL250005074508 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 630) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/630 `/scratch/stefan/7916156/working/3D/630' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)[C@@H]2C[C@H]2C)C1) `REAL250005074508.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074508/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074508 none C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)[C@@H]2C[C@H]2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 1, 6, 6, 17, 17, 17, 32, 32, 32, 32, 32, 1, 1, 1, 1, 6, 6, 25, 25, 25, 25, 25, 1, 6, 6, 6, 17, 32, 1, 1, 1, 25, 25, 25, 25, 25, 1, 1] 72 rigid atoms, others: [1, 37, 38, 12, 13, 14, 15, 23, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36]) total number of confs: 134 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074508 none C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)[C@@H]2C[C@H]2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [19, 6, 19, 6, 1, 6, 1, 1, 1, 1, 1, 1, 19, 32, 32, 32, 47, 47, 72, 72, 72, 72, 72, 32, 19, 19, 19, 6, 1, 32, 32, 32, 72, 72, 72, 72, 72, 32, 32] 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, 33, 34, 35, 36, 37, 38]) total number of confs: 249 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074508 none C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)[C@@H]2C[C@H]2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [49, 25, 49, 49, 66, 66, 66, 72, 72, 72, 72, 72, 25, 25, 9, 1, 9, 1, 1, 1, 1, 1, 1, 25, 49, 49, 49, 66, 72, 25, 25, 25, 1, 1, 2, 2, 2, 25, 25] 72 rigid atoms, others: [32, 33, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38]) total number of confs: 230 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074508 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074508 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074508/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074508 Building REAL250005074509 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074509' /scratch/stefan/7916156/working/building/REAL250005074509 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074509 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074509/0 /scratch/stefan/7916156/working/building/REAL250005074509 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 631) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/631 `/scratch/stefan/7916156/working/3D/631' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(F)C(=O)N1CC([C@H](C)NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074509.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074509.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074509/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074509 none CCC(F)C(=O)N1CC([C@H](C)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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 15, 1, 11, 8, 5, 5, 5, 7, 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, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [119, 117, 56, 117, 33, 56, 33, 33, 18, 7, 18, 18, 7, 1, 7, 1, 1, 1, 1, 1, 1, 33, 119, 119, 119, 119, 119, 117, 33, 33, 33, 18, 18, 18, 7, 1, 33, 33] 119 rigid atoms, others: [35, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37]) total number of confs: 452 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074509 none CCC(F)C(=O)N1CC([C@H](C)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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 15, 1, 11, 8, 5, 5, 5, 7, 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, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [42, 31, 5, 31, 1, 5, 1, 1, 1, 1, 7, 7, 7, 18, 18, 18, 33, 33, 33, 33, 33, 1, 50, 50, 50, 50, 50, 31, 1, 1, 1, 7, 7, 7, 18, 33, 1, 1] 119 rigid atoms, others: [4, 37, 6, 7, 8, 9, 21, 36, 28, 29, 30] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35]) total number of confs: 325 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074509 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074509 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074509/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074509 Building REAL250005074510 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074510' /scratch/stefan/7916156/working/building/REAL250005074510 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074510 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074510/0 /scratch/stefan/7916156/working/building/REAL250005074510 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 632) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/632 `/scratch/stefan/7916156/working/3D/632' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)CCCF)C1) `REAL250005074510.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074510/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074510 none C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)CCCF)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 5, 15, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 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: [6, 1, 6, 6, 17, 17, 17, 31, 31, 31, 31, 31, 1, 1, 1, 1, 6, 6, 33, 46, 90, 1, 6, 6, 6, 17, 31, 1, 1, 1, 33, 33, 54, 54, 86, 85, 1, 1] 201 rigid atoms, others: [1, 36, 37, 12, 13, 14, 15, 21, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35]) total number of confs: 484 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074510 none C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)CCCF)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 5, 15, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 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: [13, 4, 13, 4, 1, 4, 1, 1, 1, 1, 1, 1, 13, 31, 31, 31, 62, 62, 173, 191, 201, 31, 13, 13, 13, 4, 1, 31, 31, 31, 173, 173, 201, 201, 201, 201, 31, 31] 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, 35, 36, 37]) total number of confs: 901 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074510 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074510 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074510/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074510 Building REAL250005074511 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074511' /scratch/stefan/7916156/working/building/REAL250005074511 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074511 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074511/0 /scratch/stefan/7916156/working/building/REAL250005074511 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 633) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/633 `/scratch/stefan/7916156/working/3D/633' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)[C@H]2C[C@@H]2C)C1) `REAL250005074511.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074511/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074511 none C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)[C@H]2C[C@@H]2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 18, 18, 18, 40, 40, 40, 40, 40, 1, 1, 1, 1, 6, 6, 29, 29, 29, 29, 29, 1, 6, 6, 6, 18, 40, 1, 1, 1, 29, 29, 29, 29, 29, 1, 1] 79 rigid atoms, others: [1, 37, 38, 12, 13, 14, 15, 23, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36]) total number of confs: 154 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074511 none C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)[C@H]2C[C@@H]2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [23, 9, 23, 9, 1, 9, 1, 1, 1, 1, 1, 1, 23, 40, 40, 40, 59, 59, 79, 79, 79, 79, 79, 40, 23, 23, 23, 9, 1, 40, 40, 40, 79, 79, 79, 79, 79, 40, 40] 79 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 273 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.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: REAL250005074511 none C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)[C@H]2C[C@@H]2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [51, 29, 51, 51, 71, 71, 71, 79, 79, 79, 79, 79, 29, 29, 10, 1, 10, 1, 1, 1, 1, 1, 1, 29, 51, 51, 51, 71, 79, 29, 29, 29, 1, 1, 2, 2, 2, 29, 29] 79 rigid atoms, others: [32, 33, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38]) total number of confs: 241 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074511 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074511 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074511/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074511 Building REAL250005074512 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074512' /scratch/stefan/7916156/working/building/REAL250005074512 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074512 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074512/0 /scratch/stefan/7916156/working/building/REAL250005074512 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 634) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/634 `/scratch/stefan/7916156/working/3D/634' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)CO)C1) `REAL250005074512.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074512/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074512 none C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)CO)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 4, 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: [6, 1, 6, 6, 16, 16, 16, 30, 30, 30, 30, 30, 1, 1, 1, 1, 4, 4, 19, 1, 6, 6, 6, 16, 30, 1, 1, 1, 19, 19, 57, 1, 1] 147 rigid atoms, others: [32, 1, 12, 13, 14, 15, 19, 25, 26, 27, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 20, 21, 22, 23, 24, 28, 29, 30]) total number of confs: 189 number of broken/clashed sets: 14 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074512 none C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)CO)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 4, 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: [17, 7, 17, 7, 1, 7, 1, 1, 1, 1, 1, 1, 17, 30, 30, 30, 41, 41, 49, 30, 17, 17, 17, 8, 1, 30, 30, 30, 49, 49, 147, 30, 30] 147 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 24] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 336 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074512 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074512 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074512/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074512 Building REAL250005074513 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074513' /scratch/stefan/7916156/working/building/REAL250005074513 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074513 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074513/0 /scratch/stefan/7916156/working/building/REAL250005074513 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 635) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/635 `/scratch/stefan/7916156/working/3D/635' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2CCO2)C1) `REAL250005074513.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074513/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074513 none C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2CCO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 18, 18, 18, 34, 34, 34, 34, 34, 1, 1, 1, 1, 7, 7, 27, 27, 27, 1, 6, 6, 6, 18, 34, 1, 1, 1, 27, 27, 27, 27, 27, 1, 1] 70 rigid atoms, others: [1, 35, 36, 12, 13, 14, 15, 21, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34]) total number of confs: 137 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074513 none C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2CCO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [18, 7, 18, 7, 1, 7, 1, 1, 1, 1, 1, 1, 18, 34, 34, 34, 52, 52, 70, 70, 70, 34, 18, 18, 18, 7, 1, 34, 34, 34, 70, 70, 70, 70, 70, 34, 34] 70 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: 238 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.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: REAL250005074513 none C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2CCO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [53, 27, 53, 53, 66, 66, 66, 70, 70, 70, 70, 70, 27, 27, 10, 1, 10, 1, 1, 1, 1, 27, 53, 53, 53, 66, 70, 27, 27, 27, 1, 1, 1, 1, 1, 27, 27] 70 rigid atoms, others: [32, 33, 34, 15, 17, 18, 19, 20, 30, 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, 35, 36]) total number of confs: 217 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074513 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074513 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074513/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074513 Building REAL250005074514 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074514' /scratch/stefan/7916156/working/building/REAL250005074514 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074514 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074514/0 /scratch/stefan/7916156/working/building/REAL250005074514 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 636) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/636 `/scratch/stefan/7916156/working/3D/636' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2COC2)C1) `REAL250005074514.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074514/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074514 none C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2COC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 15, 15, 15, 26, 26, 26, 26, 26, 1, 1, 1, 1, 4, 4, 12, 12, 12, 1, 6, 6, 6, 15, 26, 1, 1, 1, 12, 12, 12, 12, 12, 1, 1] 49 rigid atoms, others: [1, 35, 36, 12, 13, 14, 15, 21, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34]) total number of confs: 89 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074514 none C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2COC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [17, 7, 17, 7, 1, 7, 1, 1, 1, 1, 1, 1, 17, 26, 26, 26, 36, 36, 49, 49, 49, 26, 17, 17, 17, 7, 1, 26, 26, 26, 49, 49, 49, 49, 49, 26, 26] 49 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: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074514 none C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2COC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [30, 12, 30, 30, 47, 47, 47, 49, 49, 49, 49, 49, 12, 12, 7, 1, 7, 1, 1, 1, 1, 12, 30, 30, 30, 47, 49, 12, 12, 12, 1, 1, 1, 1, 1, 12, 12] 49 rigid atoms, others: [32, 33, 34, 15, 17, 18, 19, 20, 30, 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, 35, 36]) total number of confs: 159 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074514 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074514 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074514/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074514 Building REAL250005074515 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074515' /scratch/stefan/7916156/working/building/REAL250005074515 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074515 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074515/0 /scratch/stefan/7916156/working/building/REAL250005074515 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 637) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/637 `/scratch/stefan/7916156/working/3D/637' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C=CCO)C1) `REAL250005074515.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074515/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074515 none C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C=CCO)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 1, 1, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 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 348 conformations in input total number of sets (complete confs): 348 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 18, 18, 18, 42, 42, 42, 42, 42, 1, 1, 1, 1, 6, 6, 25, 25, 69, 1, 6, 6, 6, 18, 42, 1, 1, 1, 25, 25, 69, 69, 207, 1, 1] 348 rigid atoms, others: [1, 35, 36, 12, 13, 14, 15, 21, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34]) total number of confs: 529 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074515 none C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C=CCO)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 1, 1, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 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 348 conformations in input total number of sets (complete confs): 348 using faster count positions algorithm for large data unique positions, atoms: [22, 8, 22, 8, 1, 8, 1, 1, 1, 1, 1, 1, 22, 42, 42, 42, 71, 71, 104, 104, 116, 42, 22, 22, 22, 8, 1, 42, 42, 42, 104, 104, 116, 116, 348, 42, 42] 348 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: 760 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074515 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074515 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074515/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074515 Building REAL250005074516 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074516' /scratch/stefan/7916156/working/building/REAL250005074516 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074516 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074516/0 /scratch/stefan/7916156/working/building/REAL250005074516 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 638) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/638 `/scratch/stefan/7916156/working/3D/638' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC=CC(=O)N1CC([C@H](C)NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074516.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074516/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074516 none CCC=CC(=O)N1CC([C@H](C)NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 1, 1, 11, 8, 5, 5, 5, 7, 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, 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 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [102, 87, 87, 59, 35, 59, 35, 35, 19, 6, 19, 19, 6, 1, 6, 1, 1, 1, 1, 1, 1, 35, 102, 102, 102, 102, 102, 87, 87, 35, 35, 35, 19, 19, 19, 7, 1, 35, 35] 102 rigid atoms, others: [36, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 392 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074516 none CCC=CC(=O)N1CC([C@H](C)NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 1, 1, 11, 8, 5, 5, 5, 7, 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, 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 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [54, 32, 32, 6, 1, 6, 1, 1, 1, 1, 5, 5, 5, 16, 16, 16, 35, 35, 35, 35, 35, 1, 54, 54, 54, 54, 54, 32, 32, 1, 1, 1, 5, 5, 5, 16, 35, 1, 1] 102 rigid atoms, others: [4, 37, 6, 7, 8, 9, 21, 38, 29, 30, 31] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36]) total number of confs: 264 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074516 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074516 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074516/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074516 Building REAL250005074517 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074517' /scratch/stefan/7916156/working/building/REAL250005074517 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074517 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074517/0 /scratch/stefan/7916156/working/building/REAL250005074517 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 639) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/639 `/scratch/stefan/7916156/working/3D/639' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCC(=O)N1CC([C@H](C)NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074517.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074517/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074517 none C#CCCC(=O)N1CC([C@H](C)NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 7, 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, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 132 conformations in input total number of sets (complete confs): 132 using faster count positions algorithm for large data unique positions, atoms: [132, 132, 122, 67, 41, 67, 41, 41, 20, 6, 20, 20, 6, 1, 6, 1, 1, 1, 1, 1, 1, 41, 132, 132, 132, 122, 122, 41, 41, 41, 20, 20, 20, 6, 1, 41, 41] 132 rigid atoms, others: [34, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36]) total number of confs: 533 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074517 none C#CCCC(=O)N1CC([C@H](C)NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 7, 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, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 132 conformations in input total number of sets (complete confs): 132 using faster count positions algorithm for large data unique positions, atoms: [47, 47, 28, 6, 1, 6, 1, 1, 1, 1, 6, 6, 6, 18, 18, 18, 41, 41, 41, 41, 41, 1, 47, 47, 47, 28, 28, 1, 1, 1, 6, 6, 6, 18, 41, 1, 1] 132 rigid atoms, others: [35, 4, 6, 7, 8, 9, 21, 36, 27, 28, 29] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34]) total number of confs: 283 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074517 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074517 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074517/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074517 Building REAL250005074518 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074518' /scratch/stefan/7916156/working/building/REAL250005074518 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074518 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074518/0 /scratch/stefan/7916156/working/building/REAL250005074518 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 640) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/640 `/scratch/stefan/7916156/working/3D/640' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(O)C(=O)N1CC([C@H](C)NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074518.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074518/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074518 none C=CC(O)C(=O)N1CC([C@H](C)NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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: [1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 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, 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] 1 hydrogens need rotated 279 conformations in input total number of sets (complete confs): 279 using faster count positions algorithm for large data unique positions, atoms: [93, 93, 51, 93, 32, 51, 32, 32, 20, 7, 20, 20, 7, 1, 7, 1, 1, 1, 1, 1, 1, 32, 93, 93, 93, 93, 279, 32, 32, 32, 20, 20, 20, 7, 1, 32, 32] 279 rigid atoms, others: [34, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36]) total number of confs: 643 number of broken/clashed sets: 24 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074518 none C=CC(O)C(=O)N1CC([C@H](C)NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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: [1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 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, 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] 1 hydrogens need rotated 279 conformations in input total number of sets (complete confs): 279 using faster count positions algorithm for large data unique positions, atoms: [48, 29, 6, 29, 1, 6, 1, 1, 1, 1, 6, 6, 6, 17, 17, 17, 32, 32, 32, 32, 32, 1, 48, 48, 48, 29, 87, 1, 1, 1, 6, 6, 6, 17, 32, 1, 1] 279 rigid atoms, others: [35, 4, 6, 7, 8, 9, 21, 36, 27, 28, 29] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34]) total number of confs: 318 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074518 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074518 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074518/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074518 Building REAL250005074519 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074519' /scratch/stefan/7916156/working/building/REAL250005074519 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074519 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074519/0 /scratch/stefan/7916156/working/building/REAL250005074519 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 641) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/641 `/scratch/stefan/7916156/working/3D/641' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)C(=O)N1CC([C@H](C)NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074519.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074519.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074519/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074519 none CC(O)C(=O)N1CC([C@H](C)NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 12, 1, 11, 8, 5, 5, 5, 7, 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, 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] 1 hydrogens need rotated 177 conformations in input total number of sets (complete confs): 177 using faster count positions algorithm for large data unique positions, atoms: [59, 36, 59, 27, 36, 27, 27, 17, 7, 17, 17, 7, 1, 7, 1, 1, 1, 1, 1, 1, 27, 59, 59, 59, 59, 177, 27, 27, 27, 17, 17, 17, 7, 1, 27, 27] 177 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: 415 number of broken/clashed sets: 31 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074519 none CC(O)C(=O)N1CC([C@H](C)NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 12, 1, 11, 8, 5, 5, 5, 7, 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, 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] 1 hydrogens need rotated 177 conformations in input total number of sets (complete confs): 177 using faster count positions algorithm for large data unique positions, atoms: [19, 6, 19, 1, 6, 1, 1, 1, 1, 6, 6, 6, 15, 15, 15, 27, 27, 27, 27, 27, 1, 19, 19, 19, 19, 57, 1, 1, 1, 6, 6, 6, 15, 27, 1, 1] 177 rigid atoms, others: [34, 3, 5, 6, 7, 8, 35, 20, 26, 27, 28] set([0, 1, 2, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33]) total number of confs: 186 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074519 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074519 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074519/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074519 Building REAL250005074520 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074520' /scratch/stefan/7916156/working/building/REAL250005074520 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074520 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074520/0 /scratch/stefan/7916156/working/building/REAL250005074520 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 642) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/642 `/scratch/stefan/7916156/working/3D/642' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)C(=O)N1CC([C@H](C)NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074520.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074520/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074520 none CC(=O)C(=O)N1CC([C@H](C)NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 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 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [61, 45, 61, 31, 45, 31, 31, 15, 7, 15, 15, 7, 1, 7, 1, 1, 1, 1, 1, 1, 31, 61, 61, 61, 31, 31, 31, 15, 15, 15, 7, 1, 31, 31] 61 rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33]) total number of confs: 208 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074520 none CC(=O)C(=O)N1CC([C@H](C)NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 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 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [17, 4, 17, 1, 4, 1, 1, 1, 1, 6, 6, 6, 20, 20, 20, 31, 31, 31, 31, 31, 1, 17, 17, 17, 1, 1, 1, 6, 6, 6, 20, 31, 1, 1] 61 rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 20, 24, 25, 26] set([0, 1, 2, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 27, 28, 29, 30, 31]) total number of confs: 115 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074520 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074520 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074520/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074520 Building REAL250005074521 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074521' /scratch/stefan/7916156/working/building/REAL250005074521 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074521 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074521/0 /scratch/stefan/7916156/working/building/REAL250005074521 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 643) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/643 `/scratch/stefan/7916156/working/3D/643' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2(F)CC2)C1) `REAL250005074521.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074521/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074521 none C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2(F)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 15, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 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 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 19, 19, 19, 37, 37, 37, 37, 37, 1, 1, 1, 1, 6, 6, 23, 23, 23, 1, 6, 6, 6, 19, 37, 1, 1, 1, 23, 23, 23, 23, 1, 1] 71 rigid atoms, others: [1, 34, 35, 12, 13, 14, 15, 21, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 30, 31, 32, 33]) total number of confs: 139 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074521 none C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2(F)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 15, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 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 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [19, 7, 19, 7, 1, 7, 1, 1, 1, 1, 1, 1, 19, 37, 37, 37, 56, 56, 71, 71, 71, 37, 19, 19, 19, 7, 1, 37, 37, 37, 71, 71, 71, 71, 37, 37] 71 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: 250 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.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: REAL250005074521 none C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2(F)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 15, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 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 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [46, 23, 46, 46, 68, 68, 68, 71, 71, 71, 71, 71, 23, 23, 8, 1, 8, 1, 1, 1, 1, 23, 46, 46, 46, 68, 71, 23, 23, 23, 1, 1, 1, 1, 23, 23] 71 rigid atoms, others: [32, 33, 15, 17, 18, 19, 20, 30, 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, 34, 35]) total number of confs: 230 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074521 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074521 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074521/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074521 Building REAL250005074522 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074522' /scratch/stefan/7916156/working/building/REAL250005074522 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074522 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074522/0 /scratch/stefan/7916156/working/building/REAL250005074522 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 644) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/644 `/scratch/stefan/7916156/working/3D/644' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=C(F)C(=O)N1CC([C@H](C)NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074522.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074522.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074522/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074522 none CC=C(F)C(=O)N1CC([C@H](C)NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 11, 8, 5, 5, 5, 7, 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, 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 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 30, 43, 25, 30, 25, 25, 13, 5, 13, 13, 5, 1, 5, 1, 1, 1, 1, 1, 1, 25, 43, 43, 43, 43, 25, 25, 25, 13, 13, 13, 5, 1, 25, 25] 43 rigid atoms, others: [33, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35]) total number of confs: 145 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074522 none CC=C(F)C(=O)N1CC([C@H](C)NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 11, 8, 5, 5, 5, 7, 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, 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 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 3, 15, 1, 3, 1, 1, 1, 1, 6, 6, 6, 16, 16, 16, 25, 25, 25, 25, 25, 1, 16, 16, 16, 15, 1, 1, 1, 6, 6, 6, 16, 25, 1, 1] 43 rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 21, 26, 27, 28] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 29, 30, 31, 32, 33]) total number of confs: 104 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074522 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074522 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074522/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074522 Building REAL250005074523 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074523' /scratch/stefan/7916156/working/building/REAL250005074523 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074523 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074523/0 /scratch/stefan/7916156/working/building/REAL250005074523 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 645) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/645 `/scratch/stefan/7916156/working/3D/645' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CO)C(=O)N1CC([C@H](C)NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074523.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074523/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074523 none CC(CO)C(=O)N1CC([C@H](C)NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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 225 conformations in input total number of sets (complete confs): 225 using faster count positions algorithm for large data unique positions, atoms: [71, 52, 71, 75, 37, 52, 37, 37, 20, 7, 20, 20, 7, 1, 7, 1, 1, 1, 1, 1, 1, 37, 71, 71, 71, 71, 75, 75, 225, 37, 37, 37, 20, 20, 20, 7, 1, 37, 37] 225 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: 512 number of broken/clashed sets: 19 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074523 none CC(CO)C(=O)N1CC([C@H](C)NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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 225 conformations in input total number of sets (complete confs): 225 using faster count positions algorithm for large data unique positions, atoms: [18, 7, 18, 40, 1, 7, 1, 1, 1, 1, 6, 6, 6, 18, 18, 18, 37, 37, 37, 37, 37, 1, 18, 18, 18, 18, 40, 40, 120, 1, 1, 1, 6, 6, 6, 18, 37, 1, 1] 225 rigid atoms, others: [4, 37, 6, 7, 8, 9, 21, 38, 29, 30, 31] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36]) total number of confs: 351 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074523 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074523 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074523/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074523 Building REAL250005074524 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074524' /scratch/stefan/7916156/working/building/REAL250005074524 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074524 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074524/0 /scratch/stefan/7916156/working/building/REAL250005074524 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 646) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/646 `/scratch/stefan/7916156/working/3D/646' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2(O)CC2)C1) `REAL250005074524.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074524/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074524 none C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2(O)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 18, 18, 18, 35, 35, 35, 35, 35, 1, 1, 1, 1, 6, 6, 25, 25, 25, 1, 6, 6, 6, 18, 35, 1, 1, 1, 75, 25, 25, 25, 25, 1, 1] 201 rigid atoms, others: [1, 35, 36, 12, 13, 14, 15, 21, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34]) total number of confs: 213 number of broken/clashed sets: 21 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074524 none C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2(O)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 7, 1, 7, 1, 1, 1, 1, 1, 1, 20, 35, 35, 35, 50, 50, 67, 67, 67, 35, 20, 20, 20, 8, 1, 35, 35, 35, 201, 67, 67, 67, 67, 35, 35] 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, 35, 36]) total number of confs: 439 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.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: REAL250005074524 none C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2(O)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [48, 25, 48, 48, 63, 63, 63, 67, 67, 67, 67, 67, 25, 25, 8, 1, 8, 1, 1, 1, 1, 25, 48, 48, 48, 63, 67, 25, 25, 25, 6, 1, 1, 1, 1, 25, 25] 201 rigid atoms, others: [32, 33, 34, 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, 35, 36]) total number of confs: 215 number of broken/clashed sets: 21 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074524 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074524 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074524/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074524 Building REAL250005074525 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074525' /scratch/stefan/7916156/working/building/REAL250005074525 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074525 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074525/0 /scratch/stefan/7916156/working/building/REAL250005074525 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 647) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/647 `/scratch/stefan/7916156/working/3D/647' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=CCC2)C1) `REAL250005074525.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074525/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074525 none C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 16, 16, 16, 24, 24, 24, 24, 24, 1, 1, 1, 1, 6, 6, 15, 15, 15, 1, 6, 6, 6, 16, 24, 1, 1, 1, 15, 15, 15, 15, 15, 1, 1] 31 rigid atoms, others: [1, 35, 36, 12, 13, 14, 15, 21, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34]) total number of confs: 85 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074525 none C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [13, 5, 13, 5, 1, 5, 1, 1, 1, 1, 1, 1, 13, 24, 24, 24, 31, 31, 31, 31, 31, 24, 13, 13, 13, 5, 1, 24, 24, 24, 31, 31, 31, 31, 31, 24, 24] 31 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: 109 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.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: REAL250005074525 none C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [22, 15, 22, 22, 29, 29, 29, 31, 31, 31, 31, 31, 15, 15, 7, 1, 7, 1, 1, 1, 1, 15, 22, 22, 22, 29, 31, 15, 15, 15, 1, 1, 1, 1, 1, 15, 15] 31 rigid atoms, others: [32, 33, 34, 15, 17, 18, 19, 20, 30, 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, 35, 36]) total number of confs: 84 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074525 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074525 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074525/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074525 Building REAL250005074526 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074526' /scratch/stefan/7916156/working/building/REAL250005074526 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074526 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074526/0 /scratch/stefan/7916156/working/building/REAL250005074526 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 648) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/648 `/scratch/stefan/7916156/working/3D/648' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CF)C(=O)N1CC([C@H](C)NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074526.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074526/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074526 none CC(CF)C(=O)N1CC([C@H](C)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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 15, 1, 11, 8, 5, 5, 5, 7, 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, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [75, 55, 75, 76, 36, 55, 36, 36, 19, 7, 19, 19, 7, 1, 7, 1, 1, 1, 1, 1, 1, 36, 75, 75, 75, 75, 76, 76, 36, 36, 36, 19, 19, 19, 7, 1, 36, 36] 76 rigid atoms, others: [35, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37]) total number of confs: 292 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074526 none CC(CF)C(=O)N1CC([C@H](C)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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 15, 1, 11, 8, 5, 5, 5, 7, 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, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [18, 7, 18, 43, 1, 7, 1, 1, 1, 1, 6, 6, 6, 18, 18, 18, 36, 36, 36, 36, 36, 1, 18, 18, 18, 18, 43, 43, 1, 1, 1, 6, 6, 6, 18, 36, 1, 1] 76 rigid atoms, others: [4, 37, 6, 7, 8, 9, 21, 36, 28, 29, 30] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35]) total number of confs: 236 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074526 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074526 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074526/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074526 Building REAL250005074527 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074527' /scratch/stefan/7916156/working/building/REAL250005074527 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074527 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074527/0 /scratch/stefan/7916156/working/building/REAL250005074527 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 649) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/649 `/scratch/stefan/7916156/working/3D/649' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC(=O)N1CC([C@H](C)NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074527.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074527/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074527 none CC=CC(=O)N1CC([C@H](C)NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 1, 1, 11, 8, 5, 5, 5, 7, 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, 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 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 31, 25, 31, 25, 25, 14, 6, 14, 14, 6, 1, 6, 1, 1, 1, 1, 1, 1, 25, 39, 39, 39, 39, 39, 25, 25, 25, 14, 14, 14, 6, 1, 25, 25] 39 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: 135 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074527 none CC=CC(=O)N1CC([C@H](C)NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 1, 1, 11, 8, 5, 5, 5, 7, 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, 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 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 5, 1, 5, 1, 1, 1, 1, 6, 6, 6, 17, 17, 17, 25, 25, 25, 25, 25, 1, 15, 15, 15, 14, 14, 1, 1, 1, 6, 6, 6, 17, 25, 1, 1] 39 rigid atoms, others: [34, 3, 5, 6, 7, 8, 35, 20, 26, 27, 28] set([0, 1, 2, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33]) total number of confs: 103 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074527 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074527 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074527/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074527 Building REAL250005074528 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074528' /scratch/stefan/7916156/working/building/REAL250005074528 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074528 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074528/0 /scratch/stefan/7916156/working/building/REAL250005074528 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 650) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/650 `/scratch/stefan/7916156/working/3D/650' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C=CCF)C1) `REAL250005074528.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074528.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074528/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074528 none C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C=CCF)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 1, 1, 5, 15, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 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 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 15, 15, 15, 32, 32, 32, 32, 32, 1, 1, 1, 1, 6, 6, 21, 21, 49, 1, 6, 6, 6, 15, 32, 1, 1, 1, 21, 21, 49, 49, 1, 1] 89 rigid atoms, others: [1, 34, 35, 12, 13, 14, 15, 21, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 30, 31, 32, 33]) total number of confs: 235 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074528 none C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C=CCF)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 1, 1, 5, 15, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 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 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [18, 6, 18, 6, 1, 6, 1, 1, 1, 1, 1, 1, 18, 32, 32, 32, 55, 55, 80, 80, 89, 32, 18, 18, 18, 7, 1, 32, 32, 32, 80, 80, 89, 89, 32, 32] 89 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: 331 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074528 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074528 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074528/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074528 Building REAL250005074529 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074529' /scratch/stefan/7916156/working/building/REAL250005074529 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types Protomer extracton resulted in 0 protomers Marking REAL250005074529 as failed and skipping /scratch/stefan/7916156/working /scratch/stefan/7916156 `/scratch/stefan/7916156/working/building/REAL250005074529' -> `/scratch/stefan/7916156/failed/REAL250005074529' Building REAL250005074530 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074530' /scratch/stefan/7916156/working/building/REAL250005074530 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074530 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074530/0 /scratch/stefan/7916156/working/building/REAL250005074530 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 651) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/651 `/scratch/stefan/7916156/working/3D/651' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)C(=O)N1CC([C@H](C)NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074530.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074530/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074530 none C[C@H](O)C(=O)N1CC([C@H](C)NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 168 conformations in input total number of sets (complete confs): 168 using faster count positions algorithm for large data unique positions, atoms: [56, 35, 56, 56, 28, 35, 28, 28, 15, 6, 15, 15, 6, 1, 6, 1, 1, 1, 1, 1, 1, 28, 56, 56, 56, 168, 28, 28, 28, 15, 15, 15, 6, 1, 28, 28] 168 rigid atoms, others: [33, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35]) total number of confs: 395 number of broken/clashed sets: 30 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074530 none C[C@H](O)C(=O)N1CC([C@H](C)NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 168 conformations in input total number of sets (complete confs): 168 using faster count positions algorithm for large data unique positions, atoms: [20, 6, 20, 20, 1, 6, 1, 1, 1, 1, 6, 6, 6, 16, 16, 16, 28, 28, 28, 28, 28, 1, 20, 20, 20, 60, 1, 1, 1, 6, 6, 6, 16, 28, 1, 1] 168 rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 21, 26, 27, 28] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 29, 30, 31, 32, 33]) total number of confs: 191 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074530 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074530 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074530/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074530 Building REAL250005074531 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074531' /scratch/stefan/7916156/working/building/REAL250005074531 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074531 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074531/0 /scratch/stefan/7916156/working/building/REAL250005074531 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 652) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/652 `/scratch/stefan/7916156/working/3D/652' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CON=CC(=O)N1CC([C@H](C)NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074531.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074531/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074531 none CON=CC(=O)N1CC([C@H](C)NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 8, 1, 1, 11, 8, 5, 5, 5, 7, 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, 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 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [94, 94, 94, 53, 34, 53, 34, 34, 20, 7, 20, 20, 7, 1, 7, 1, 1, 1, 1, 1, 1, 34, 94, 94, 94, 94, 34, 34, 34, 20, 20, 20, 7, 1, 34, 34] 94 rigid atoms, others: [33, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35]) total number of confs: 304 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074531 none CON=CC(=O)N1CC([C@H](C)NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 8, 1, 1, 11, 8, 5, 5, 5, 7, 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, 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 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [45, 33, 33, 6, 1, 6, 1, 1, 1, 1, 7, 7, 7, 19, 19, 19, 34, 34, 34, 34, 34, 1, 46, 46, 46, 33, 1, 1, 1, 7, 7, 7, 19, 34, 1, 1] 94 rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 21, 26, 27, 28] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 29, 30, 31, 32, 33]) total number of confs: 184 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074531 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074531 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074531/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074531 Building REAL250005074532 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074532' /scratch/stefan/7916156/working/building/REAL250005074532 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074532 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074532/0 /scratch/stefan/7916156/working/building/REAL250005074532 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 653) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/653 `/scratch/stefan/7916156/working/3D/653' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)[C@@H]2C[C@H]2C)C1) `REAL250005074532.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074532/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074532 none C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)[C@@H]2C[C@H]2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 1, 6, 6, 17, 17, 17, 32, 32, 32, 32, 32, 1, 1, 1, 1, 6, 6, 25, 25, 25, 25, 25, 1, 6, 6, 6, 17, 32, 1, 1, 1, 25, 25, 25, 25, 25, 1, 1] 72 rigid atoms, others: [1, 37, 38, 12, 13, 14, 15, 23, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36]) total number of confs: 134 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074532 none C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)[C@@H]2C[C@H]2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [19, 6, 19, 6, 1, 6, 1, 1, 1, 1, 1, 1, 19, 32, 32, 32, 47, 47, 72, 72, 72, 72, 72, 32, 19, 19, 19, 6, 1, 32, 32, 32, 72, 72, 72, 72, 72, 32, 32] 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, 33, 34, 35, 36, 37, 38]) total number of confs: 249 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074532 none C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)[C@@H]2C[C@H]2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [49, 25, 49, 49, 66, 66, 66, 72, 72, 72, 72, 72, 25, 25, 9, 1, 9, 1, 1, 1, 1, 1, 1, 25, 49, 49, 49, 66, 72, 25, 25, 25, 1, 1, 2, 2, 2, 25, 25] 72 rigid atoms, others: [32, 33, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38]) total number of confs: 230 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074532 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074532 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074532/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074532 Building REAL250005074533 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074533' /scratch/stefan/7916156/working/building/REAL250005074533 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074533 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074533/0 /scratch/stefan/7916156/working/building/REAL250005074533 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 654) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/654 `/scratch/stefan/7916156/working/3D/654' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C(C)(C)O)C1) `REAL250005074533.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074533/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074533 none C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C(C)(C)O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 14, 14, 14, 21, 21, 21, 21, 21, 1, 1, 1, 1, 3, 3, 10, 10, 10, 1, 6, 6, 6, 14, 21, 1, 1, 1, 10, 10, 10, 10, 10, 10, 30, 1, 1] 108 rigid atoms, others: [1, 37, 38, 12, 13, 14, 15, 21, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 120 number of broken/clashed sets: 44 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074533 none C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C(C)(C)O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [13, 6, 13, 6, 1, 6, 1, 1, 1, 1, 1, 1, 13, 21, 21, 21, 26, 26, 36, 36, 36, 21, 13, 13, 13, 6, 1, 21, 21, 21, 36, 36, 36, 36, 36, 36, 108, 21, 21] 108 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, 37, 38]) total number of confs: 251 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074533 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074533 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074533/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074533 Building REAL250005074534 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074534' /scratch/stefan/7916156/working/building/REAL250005074534 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074534 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074534/0 /scratch/stefan/7916156/working/building/REAL250005074534 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 655) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/655 `/scratch/stefan/7916156/working/3D/655' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)CC(=O)N1CC([C@H](C)NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074534.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074534/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074534 none C=C(C)CC(=O)N1CC([C@H](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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 7, 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, 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 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [125, 125, 125, 62, 39, 62, 39, 39, 20, 6, 20, 20, 6, 1, 6, 1, 1, 1, 1, 1, 1, 39, 125, 125, 125, 125, 125, 125, 125, 39, 39, 39, 20, 20, 20, 6, 1, 39, 39] 125 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: 490 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074534 none C=C(C)CC(=O)N1CC([C@H](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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 7, 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, 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 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [59, 35, 59, 6, 1, 6, 1, 1, 1, 1, 6, 6, 6, 18, 18, 18, 39, 39, 39, 39, 39, 1, 59, 59, 59, 59, 59, 35, 35, 1, 1, 1, 6, 6, 6, 18, 39, 1, 1] 125 rigid atoms, others: [4, 37, 6, 7, 8, 9, 21, 38, 29, 30, 31] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36]) total number of confs: 279 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074534 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074534 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074534/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074534 Building REAL250005074535 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074535' /scratch/stefan/7916156/working/building/REAL250005074535 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074535 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074535/0 /scratch/stefan/7916156/working/building/REAL250005074535 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 656) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/656 `/scratch/stefan/7916156/working/3D/656' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(=O)N1CC([C@H](C)NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074535.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074535.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074535/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074535 none C=CCC(=O)N1CC([C@H](C)NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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: [1, 1, 5, 1, 11, 8, 5, 5, 5, 7, 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, 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 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [100, 100, 56, 38, 56, 38, 38, 21, 8, 21, 21, 8, 1, 8, 1, 1, 1, 1, 1, 1, 38, 100, 100, 100, 100, 100, 38, 38, 38, 21, 21, 21, 8, 1, 38, 38] 100 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: 395 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074535 none C=CCC(=O)N1CC([C@H](C)NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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: [1, 1, 5, 1, 11, 8, 5, 5, 5, 7, 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, 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 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [49, 28, 6, 1, 6, 1, 1, 1, 1, 6, 6, 6, 19, 19, 19, 38, 38, 38, 38, 38, 1, 49, 49, 49, 28, 28, 1, 1, 1, 6, 6, 6, 19, 38, 1, 1] 100 rigid atoms, others: [34, 3, 5, 6, 7, 8, 35, 20, 26, 27, 28] set([0, 1, 2, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33]) total number of confs: 247 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074535 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074535 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074535/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074535 Building REAL250005074536 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074536' /scratch/stefan/7916156/working/building/REAL250005074536 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005074536 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074536/0 /scratch/stefan/7916156/working/building/REAL250005074536 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 657) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/657 `/scratch/stefan/7916156/working/3D/657' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C[NH+](C)C)C1) `REAL250005074536.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074536.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074536/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074536 none C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C[NH+](C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 7, 16, 16, 16, 28, 28, 28, 28, 28, 1, 1, 1, 1, 4, 4, 16, 16, 16, 16, 1, 7, 7, 7, 16, 28, 1, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1] 46 rigid atoms, others: [1, 39, 40, 12, 13, 14, 15, 22, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 122 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074536 none C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C[NH+](C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [16, 8, 16, 8, 1, 8, 1, 1, 1, 1, 1, 1, 16, 28, 28, 28, 33, 33, 46, 46, 46, 46, 28, 16, 16, 16, 8, 1, 28, 28, 28, 46, 46, 46, 46, 46, 46, 46, 46, 28, 28] 46 rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 27] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 178 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074536 /scratch/stefan/7916156/working /scratch/stefan/7916156 mkdir: created directory `1' /scratch/stefan/7916156/working/building/REAL250005074536/1 /scratch/stefan/7916156/working/building/REAL250005074536 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 1 (index: 658) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/658 `/scratch/stefan/7916156/working/3D/658' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)CN(C)C)C1) `REAL250005074536.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005074536.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074536/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074536 none C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)CN(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 132 conformations in input total number of sets (complete confs): 132 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 18, 18, 18, 35, 35, 35, 35, 35, 1, 1, 1, 1, 6, 6, 36, 68, 68, 1, 6, 6, 6, 18, 35, 1, 1, 1, 36, 36, 68, 68, 68, 68, 68, 68, 1, 1] 132 rigid atoms, others: [1, 38, 39, 12, 13, 14, 15, 21, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 295 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074536 none C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)CN(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [17, 6, 17, 6, 1, 6, 1, 1, 1, 1, 1, 1, 17, 35, 35, 35, 62, 62, 129, 132, 132, 35, 17, 17, 17, 6, 1, 35, 35, 35, 129, 129, 132, 132, 132, 132, 132, 132, 35, 35] 132 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, 37, 38, 39]) total number of confs: 517 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074536 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074536 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 1: /scratch/stefan/7916156/working/building/REAL250005074536/1.* 0: /scratch/stefan/7916156/working/building/REAL250005074536/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074536 Building REAL250005074537 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074537' /scratch/stefan/7916156/working/building/REAL250005074537 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074537 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074537/0 /scratch/stefan/7916156/working/building/REAL250005074537 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 659) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/659 `/scratch/stefan/7916156/working/3D/659' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)CC#N)C1) `REAL250005074537.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074537/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074537 none C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)CC#N)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 1, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 20, 20, 20, 35, 35, 35, 35, 35, 1, 1, 1, 1, 6, 6, 30, 30, 1, 6, 6, 6, 20, 35, 1, 1, 1, 30, 30, 1, 1] 79 rigid atoms, others: [32, 1, 12, 13, 14, 15, 20, 26, 27, 28, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 21, 22, 23, 24, 25, 29, 30]) total number of confs: 180 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074537 none C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)CC#N)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 1, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [17, 7, 17, 7, 1, 7, 1, 1, 1, 1, 1, 1, 17, 35, 35, 35, 53, 53, 79, 79, 35, 17, 17, 17, 8, 1, 35, 35, 35, 79, 79, 35, 35] 79 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, 32]) total number of confs: 308 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074537 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074537 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074537/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074537 Building REAL250005074538 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074538' /scratch/stefan/7916156/working/building/REAL250005074538 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074538 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074538/0 /scratch/stefan/7916156/working/building/REAL250005074538 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 660) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/660 `/scratch/stefan/7916156/working/3D/660' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2CC2F)C1) `REAL250005074538.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074538/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074538 none C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2CC2F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 5, 15, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 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 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 17, 17, 17, 27, 27, 27, 27, 27, 1, 1, 1, 1, 5, 5, 18, 18, 18, 1, 6, 6, 6, 17, 27, 1, 1, 1, 18, 18, 18, 18, 1, 1] 65 rigid atoms, others: [1, 34, 35, 12, 13, 14, 15, 21, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 30, 31, 32, 33]) total number of confs: 108 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074538 none C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2CC2F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 5, 15, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 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 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, 7, 1, 7, 1, 1, 1, 1, 1, 1, 18, 27, 27, 27, 37, 37, 65, 65, 65, 27, 18, 18, 18, 7, 1, 27, 27, 27, 65, 65, 65, 65, 27, 27] 65 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: 213 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.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: REAL250005074538 none C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2CC2F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 5, 15, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 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 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [43, 18, 43, 43, 60, 60, 60, 65, 65, 65, 65, 65, 18, 18, 9, 1, 9, 1, 1, 1, 1, 18, 43, 43, 43, 60, 65, 18, 18, 18, 1, 1, 1, 1, 18, 18] 65 rigid atoms, others: [32, 33, 15, 17, 18, 19, 20, 30, 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, 34, 35]) total number of confs: 215 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074538 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074538 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074538/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074538 Building REAL250005074539 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074539' /scratch/stefan/7916156/working/building/REAL250005074539 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074539 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074539/0 /scratch/stefan/7916156/working/building/REAL250005074539 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 661) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/661 `/scratch/stefan/7916156/working/3D/661' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)CCF)C1) `REAL250005074539.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074539/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074539 none C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)CCF)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 15, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 17, 17, 17, 34, 34, 34, 34, 34, 1, 1, 1, 1, 4, 4, 21, 36, 1, 6, 6, 6, 17, 34, 1, 1, 1, 21, 21, 36, 36, 1, 1] 97 rigid atoms, others: [1, 34, 33, 12, 13, 14, 15, 20, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 21, 22, 23, 24, 25, 29, 30, 31, 32]) total number of confs: 222 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074539 none C[C@H](NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)CCF)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 15, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [19, 7, 19, 7, 1, 7, 1, 1, 1, 1, 1, 1, 19, 34, 34, 34, 50, 50, 97, 97, 34, 19, 19, 19, 7, 1, 34, 34, 34, 97, 97, 97, 97, 34, 34] 97 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, 32, 33, 34]) total number of confs: 394 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074539 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074539 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074539/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074539 Building REAL250005074540 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074540' /scratch/stefan/7916156/working/building/REAL250005074540 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074540 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074540/0 /scratch/stefan/7916156/working/building/REAL250005074540 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 662) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/662 `/scratch/stefan/7916156/working/3D/662' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](C)C(=O)N1CC([C@H](C)NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074540.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074540.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074540/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074540 none CO[C@H](C)C(=O)N1CC([C@H](C)NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 7, 5, 1, 11, 8, 5, 5, 5, 7, 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, 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 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [84, 81, 56, 81, 81, 38, 56, 38, 38, 20, 7, 20, 20, 7, 1, 7, 1, 1, 1, 1, 1, 1, 38, 84, 84, 84, 81, 81, 81, 38, 38, 38, 20, 20, 20, 7, 1, 38, 38] 84 rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 311 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074540 none CO[C@H](C)C(=O)N1CC([C@H](C)NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 7, 5, 1, 11, 8, 5, 5, 5, 7, 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, 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 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [41, 28, 6, 28, 28, 1, 6, 1, 1, 1, 1, 6, 6, 6, 19, 19, 19, 38, 38, 38, 38, 38, 1, 41, 41, 41, 28, 28, 28, 1, 1, 1, 6, 6, 6, 19, 38, 1, 1] 84 rigid atoms, others: [5, 38, 7, 8, 9, 10, 37, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36]) total number of confs: 201 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074540 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074540 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074540/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074540 Building REAL250005074541 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074541' /scratch/stefan/7916156/working/building/REAL250005074541 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074541 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074541/0 /scratch/stefan/7916156/working/building/REAL250005074541 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 663) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/663 `/scratch/stefan/7916156/working/3D/663' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)C(=O)N1CC([C@H](C)NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074541.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074541/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074541 none C[C@@H](O)C(=O)N1CC([C@H](C)NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 159 conformations in input total number of sets (complete confs): 159 using faster count positions algorithm for large data unique positions, atoms: [53, 37, 53, 53, 27, 37, 27, 27, 17, 7, 17, 17, 7, 1, 7, 1, 1, 1, 1, 1, 1, 27, 53, 53, 53, 159, 27, 27, 27, 17, 17, 17, 8, 1, 27, 27] 159 rigid atoms, others: [33, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35]) total number of confs: 367 number of broken/clashed sets: 23 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074541 none C[C@@H](O)C(=O)N1CC([C@H](C)NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 159 conformations in input total number of sets (complete confs): 159 using faster count positions algorithm for large data unique positions, atoms: [19, 6, 19, 19, 1, 6, 1, 1, 1, 1, 5, 5, 5, 15, 15, 15, 27, 27, 27, 27, 27, 1, 19, 19, 19, 57, 1, 1, 1, 6, 6, 6, 15, 27, 1, 1] 159 rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 21, 26, 27, 28] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 29, 30, 31, 32, 33]) total number of confs: 192 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074541 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074541 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074541/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074541 Building REAL250005074542 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074542' /scratch/stefan/7916156/working/building/REAL250005074542 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074542 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074542/0 /scratch/stefan/7916156/working/building/REAL250005074542 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 664) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/664 `/scratch/stefan/7916156/working/3D/664' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C1CC1C(=O)N1CC([C@H](C)NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074542.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074542/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074542 none C=C1CC1C(=O)N1CC([C@H](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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 7, 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, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 6, 1, 6, 1, 1, 1, 1, 6, 6, 6, 19, 19, 19, 34, 34, 34, 34, 34, 1, 29, 29, 29, 29, 29, 1, 1, 1, 6, 6, 6, 19, 34, 1, 1] 79 rigid atoms, others: [35, 4, 6, 7, 8, 9, 21, 36, 27, 28, 29] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34]) total number of confs: 146 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074542 none C=C1CC1C(=O)N1CC([C@H](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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 7, 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, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 11, 11, 29, 29, 29, 55, 55, 55, 74, 74, 74, 79, 79, 79, 79, 79, 29, 1, 1, 1, 1, 1, 29, 29, 29, 55, 55, 55, 74, 79, 29, 29] 79 rigid atoms, others: [0, 1, 2, 3, 4, 22, 23, 24, 25, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 247 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.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: REAL250005074542 none C=C1CC1C(=O)N1CC([C@H](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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 7, 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, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [79, 79, 79, 45, 34, 45, 34, 34, 19, 6, 19, 19, 6, 1, 6, 1, 1, 1, 1, 1, 1, 34, 79, 79, 79, 79, 79, 34, 34, 34, 19, 19, 19, 6, 1, 34, 34] 79 rigid atoms, others: [34, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36]) total number of confs: 261 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074542 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074542 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074542/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074542 Building REAL250005074543 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074543' /scratch/stefan/7916156/working/building/REAL250005074543 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074543 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074543/0 /scratch/stefan/7916156/working/building/REAL250005074543 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 665) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/665 `/scratch/stefan/7916156/working/3D/665' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC1C(=O)N1CC([C@H](C)NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074543.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074543/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074543 none CC1=CC1C(=O)N1CC([C@H](C)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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 1, 5, 1, 11, 8, 5, 5, 5, 7, 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, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 95 conformations in input total number of sets (complete confs): 95 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 31, 6, 1, 6, 1, 1, 1, 1, 6, 6, 6, 20, 20, 20, 35, 35, 35, 35, 35, 1, 31, 31, 31, 31, 31, 1, 1, 1, 6, 6, 6, 20, 35, 1, 1] 95 rigid atoms, others: [35, 4, 6, 7, 8, 9, 21, 36, 27, 28, 29] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34]) total number of confs: 154 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074543 none CC1=CC1C(=O)N1CC([C@H](C)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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 1, 5, 1, 11, 8, 5, 5, 5, 7, 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, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 95 conformations in input total number of sets (complete confs): 95 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 11, 11, 31, 31, 31, 61, 61, 61, 89, 89, 89, 95, 95, 95, 95, 95, 31, 2, 2, 2, 1, 1, 31, 31, 31, 61, 61, 61, 89, 95, 31, 31] 95 rigid atoms, others: [0, 1, 2, 3, 4, 25, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 302 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.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: REAL250005074543 none CC1=CC1C(=O)N1CC([C@H](C)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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 1, 5, 1, 11, 8, 5, 5, 5, 7, 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, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 95 conformations in input total number of sets (complete confs): 95 using faster count positions algorithm for large data unique positions, atoms: [95, 95, 95, 53, 35, 53, 35, 35, 19, 8, 19, 19, 8, 1, 8, 1, 1, 1, 1, 1, 1, 35, 95, 95, 95, 95, 95, 35, 35, 35, 19, 19, 19, 8, 1, 35, 35] 95 rigid atoms, others: [34, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36]) total number of confs: 311 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074543 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074543 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074543/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074543 Building REAL250005074544 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074544' /scratch/stefan/7916156/working/building/REAL250005074544 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074544 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074544/0 /scratch/stefan/7916156/working/building/REAL250005074544 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 666) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/666 `/scratch/stefan/7916156/working/3D/666' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(=O)N1CC([C@H](C)NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074544.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074544/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074544 none C=CC(=O)N1CC([C@H](C)NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 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 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 21, 30, 21, 21, 14, 6, 14, 14, 6, 1, 6, 1, 1, 1, 1, 1, 1, 21, 30, 30, 30, 21, 21, 21, 14, 14, 14, 7, 1, 21, 21] 30 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32]) total number of confs: 103 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074544 none C=CC(=O)N1CC([C@H](C)NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 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 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 1, 4, 1, 1, 1, 1, 5, 5, 5, 14, 14, 14, 21, 21, 21, 21, 21, 1, 9, 9, 9, 1, 1, 1, 5, 5, 5, 14, 21, 1, 1] 30 rigid atoms, others: [32, 2, 4, 5, 6, 7, 19, 23, 24, 25, 31] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 26, 27, 28, 29, 30]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074544 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074544 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074544/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074544 Building REAL250005074545 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074545' /scratch/stefan/7916156/working/building/REAL250005074545 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074545 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074545/0 /scratch/stefan/7916156/working/building/REAL250005074545 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 667) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/667 `/scratch/stefan/7916156/working/3D/667' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC1CN(C(=O)C2=CC(=O)[N-]O2)CCC1(C)C) `REAL250005074545.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074545/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074545 none CC(=O)NCC1CN(C(=O)C2=CC(=O)[N-]O2)CCC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 28, 25, 25, 25, 10, 1, 10, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 38, 38, 38, 38, 28, 28, 25, 25, 25, 1, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25] 38 rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 99 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074545 none CC(=O)NCC1CN(C(=O)C2=CC(=O)[N-]O2)CCC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 10, 10, 4, 1, 1, 1, 1, 1, 7, 7, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 10, 10, 10, 10, 4, 4, 1, 1, 1, 25, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2] 38 rigid atoms, others: [32, 33, 34, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 27, 28, 29, 31] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 30, 35, 36, 37, 38, 39, 40]) total number of confs: 79 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074545 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074545 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074545/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074545 Building REAL250005074546 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074546' /scratch/stefan/7916156/working/building/REAL250005074546 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074546 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074546/0 /scratch/stefan/7916156/working/building/REAL250005074546 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 668) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/668 `/scratch/stefan/7916156/working/3D/668' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC(C)(C)C(CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074546.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074546.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074546/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074546 none CC(=O)N1CCC(C)(C)C(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [24, 23, 24, 23, 23, 23, 23, 23, 23, 16, 8, 7, 1, 7, 1, 1, 1, 1, 1, 1, 23, 24, 24, 24, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 16, 16, 8, 1, 23, 23] 24 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: 79 number of broken/clashed sets: 17 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074546 none CC(=O)N1CCC(C)(C)C(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 18, 18, 18, 23, 23, 23, 23, 23, 1, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 5, 5, 18, 23, 1, 1] 24 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 9, 10, 39, 40, 20, 24, 25, 26, 27] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38]) total number of confs: 81 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074546 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074546 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074546/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074546 Building REAL250005074547 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074547' /scratch/stefan/7916156/working/building/REAL250005074547 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074547 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074547/0 /scratch/stefan/7916156/working/building/REAL250005074547 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 669) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/669 `/scratch/stefan/7916156/working/3D/669' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F) `REAL250005074547.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074547/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074547 none CCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [84, 65, 65, 65, 34, 34, 34, 34, 10, 1, 10, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 84, 84, 84, 84, 84, 65, 34, 34, 1, 34, 34] 84 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: 276 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074547 none CCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [34, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 34, 34, 34, 34, 34, 1, 1, 1, 1, 34, 34, 34, 34, 34, 6, 1, 1, 34, 1, 1] 84 rigid atoms, others: [4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 27, 28, 30, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 29]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074547 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074547 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074547/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074547 Building REAL250005074548 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074548' /scratch/stefan/7916156/working/building/REAL250005074548 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074548 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074548/0 /scratch/stefan/7916156/working/building/REAL250005074548 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 670) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/670 `/scratch/stefan/7916156/working/3D/670' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F) `REAL250005074548.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074548/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074548 none CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 7, 1, 7, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 20, 20] 20 rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28]) total number of confs: 33 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074548 none CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 20, 20, 20, 20, 20, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 20, 1, 1] 20 rigid atoms, others: [3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 24, 25, 27, 28] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 26]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074548 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074548 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074548/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074548 Building REAL250005074549 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074549' /scratch/stefan/7916156/working/building/REAL250005074549 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074549 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074549/0 /scratch/stefan/7916156/working/building/REAL250005074549 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 671) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/671 `/scratch/stefan/7916156/working/3D/671' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F)C1CC1) `REAL250005074549.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074549/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074549 none O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F)C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 5, 5, 5, 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, 7, 3, 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: [50, 50, 24, 24, 24, 24, 10, 1, 10, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 50, 68, 68, 50, 24, 24, 1, 24, 24, 68, 68, 68, 68, 68] 68 rigid atoms, others: [7, 9, 10, 11, 12, 13, 14, 25] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 195 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074549 none O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F)C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 5, 5, 5, 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, 7, 3, 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: [6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 24, 24, 24, 24, 24, 1, 1, 1, 1, 6, 38, 38, 6, 1, 1, 24, 1, 1, 38, 38, 38, 38, 38] 68 rigid atoms, others: [2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 23, 24, 26, 27] set([0, 1, 32, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 25, 28, 29, 30, 31]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.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: REAL250005074549 none O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F)C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 5, 5, 5, 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, 7, 3, 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: [11, 1, 11, 11, 38, 38, 38, 38, 61, 61, 68, 68, 68, 68, 68, 38, 38, 38, 38, 1, 1, 1, 11, 38, 38, 68, 38, 38, 1, 1, 1, 1, 1] 68 rigid atoms, others: [32, 1, 19, 20, 21, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27]) total number of confs: 199 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074549 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074549 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074549/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074549 Building REAL250005074550 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074550' /scratch/stefan/7916156/working/building/REAL250005074550 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074550 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074550/0 /scratch/stefan/7916156/working/building/REAL250005074550 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 672) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/672 `/scratch/stefan/7916156/working/3D/672' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F)C1CCC1) `REAL250005074550.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074550/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074550 none O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F)C1CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 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: [56, 56, 31, 31, 31, 31, 9, 1, 9, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 56, 90, 90, 90, 56, 31, 31, 1, 31, 31, 90, 90, 90, 90, 90, 90, 90] 90 rigid atoms, others: [7, 9, 10, 11, 12, 13, 14, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 239 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074550 none O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F)C1CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 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: [5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 31, 31, 31, 31, 31, 1, 1, 1, 1, 5, 30, 30, 30, 5, 1, 1, 31, 1, 1, 30, 30, 30, 30, 30, 30, 30] 90 rigid atoms, others: [2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 24, 25, 27, 28] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 26, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 113 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.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: REAL250005074550 none O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F)C1CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 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: [13, 1, 13, 13, 30, 30, 30, 30, 84, 84, 90, 90, 90, 90, 90, 30, 30, 30, 30, 1, 1, 1, 1, 13, 30, 30, 90, 30, 30, 1, 1, 1, 1, 1, 1, 1] 90 rigid atoms, others: [32, 1, 34, 35, 33, 19, 20, 21, 22, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28]) total number of confs: 239 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074550 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074550 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074550/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074550 Building REAL250005074551 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074551' /scratch/stefan/7916156/working/building/REAL250005074551 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074551 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074551/0 /scratch/stefan/7916156/working/building/REAL250005074551 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 673) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/673 `/scratch/stefan/7916156/working/3D/673' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1CC1)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F) `REAL250005074551.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074551/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074551 none O=C(CC1CC1)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 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: [6, 6, 6, 45, 67, 67, 1, 1, 1, 1, 1, 1, 6, 6, 27, 27, 27, 27, 27, 1, 1, 1, 1, 45, 45, 67, 67, 67, 67, 67, 6, 1, 1, 27, 1, 1] 130 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 33]) total number of confs: 272 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074551 none O=C(CC1CC1)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 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: [24, 3, 1, 1, 1, 1, 24, 24, 67, 67, 67, 67, 116, 116, 130, 130, 130, 130, 130, 67, 67, 67, 67, 3, 3, 1, 1, 1, 1, 1, 24, 67, 67, 130, 67, 67] 130 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]) total number of confs: 369 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074551 none O=C(CC1CC1)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 130 conformations in input total number of sets (complete confs): 130 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 57, 107, 130, 130, 27, 27, 27, 27, 10, 1, 10, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 107, 107, 130, 130, 130, 130, 130, 57, 27, 27, 1, 27, 27] 130 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: 473 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074551 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074551 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074551/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074551 Building REAL250005074552 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074552' /scratch/stefan/7916156/working/building/REAL250005074552 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074552 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074552/0 /scratch/stefan/7916156/working/building/REAL250005074552 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 674) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/674 `/scratch/stefan/7916156/working/3D/674' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F) `REAL250005074552.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074552/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074552 none COCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 92 conformations in input total number of sets (complete confs): 92 using faster count positions algorithm for large data unique positions, atoms: [92, 92, 66, 66, 66, 25, 25, 25, 25, 9, 1, 9, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 92, 92, 92, 92, 92, 66, 25, 25, 1, 25, 25] 92 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: 293 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074552 none COCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 92 conformations in input total number of sets (complete confs): 92 using faster count positions algorithm for large data unique positions, atoms: [53, 41, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 25, 25, 25, 25, 25, 1, 1, 1, 1, 53, 53, 53, 41, 41, 6, 1, 1, 25, 1, 1] 92 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 28, 29, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 30]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074552 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074552 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074552/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074552 Building REAL250005074553 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074553' /scratch/stefan/7916156/working/building/REAL250005074553 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074553 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074553/0 /scratch/stefan/7916156/working/building/REAL250005074553 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 675) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/675 `/scratch/stefan/7916156/working/3D/675' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F) `REAL250005074553.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074553/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074553 none CCCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 138 conformations in input total number of sets (complete confs): 138 using faster count positions algorithm for large data unique positions, atoms: [138, 133, 72, 72, 72, 33, 33, 33, 33, 9, 1, 9, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 138, 138, 138, 138, 138, 133, 133, 72, 33, 33, 1, 33, 33] 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, 34]) total number of confs: 499 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074553 none CCCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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: [50, 35, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 33, 33, 33, 33, 33, 1, 1, 1, 1, 59, 59, 59, 59, 59, 35, 35, 5, 1, 1, 33, 1, 1] 138 rigid atoms, others: [33, 34, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 32, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 346 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074553 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074553 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074553/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074553 Building REAL250005074554 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074554' /scratch/stefan/7916156/working/building/REAL250005074554 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074554 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074554/0 /scratch/stefan/7916156/working/building/REAL250005074554 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 676) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/676 `/scratch/stefan/7916156/working/3D/676' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F) `REAL250005074554.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074554 none CC(C)CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 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, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 92 conformations in input total number of sets (complete confs): 92 using faster count positions algorithm for large data unique positions, atoms: [92, 88, 92, 51, 51, 51, 23, 23, 23, 23, 8, 1, 8, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 92, 92, 92, 92, 92, 92, 92, 88, 88, 51, 23, 23, 1, 23, 23] 92 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: 332 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074554 none CC(C)CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 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, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 92 conformations in input total number of sets (complete confs): 92 using faster count positions algorithm for large data unique positions, atoms: [34, 30, 41, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 23, 23, 23, 23, 23, 1, 1, 1, 1, 41, 41, 41, 41, 41, 41, 41, 30, 30, 6, 1, 1, 23, 1, 1] 92 rigid atoms, others: [33, 34, 36, 37, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35]) total number of confs: 243 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074554 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074554 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074554/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074554 Building REAL250005074555 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074555' /scratch/stefan/7916156/working/building/REAL250005074555 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074555 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074555/0 /scratch/stefan/7916156/working/building/REAL250005074555 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 677) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/677 `/scratch/stefan/7916156/working/3D/677' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F) `REAL250005074555.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074555/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074555 none CC1CC1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 7, 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, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 33, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 25, 25, 25, 25, 25, 1, 1, 1, 1, 33, 33, 33, 33, 33, 33, 33, 6, 1, 1, 25, 1, 1] 67 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 33]) total number of confs: 113 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074555 none CC1CC1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 7, 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, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 10, 10, 10, 33, 33, 33, 33, 60, 60, 67, 67, 67, 67, 67, 33, 33, 33, 33, 2, 2, 2, 1, 1, 1, 1, 10, 33, 33, 67, 33, 33] 67 rigid atoms, others: [0, 1, 2, 3, 4, 26, 27, 28, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074555 none CC1CC1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 7, 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, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 67, 49, 49, 49, 25, 25, 25, 25, 9, 1, 9, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 67, 67, 67, 67, 67, 67, 67, 49, 25, 25, 1, 25, 25] 67 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: 184 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074555 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074555 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074555/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074555 Building REAL250005074556 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074556' /scratch/stefan/7916156/working/building/REAL250005074556 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074556 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074556/0 /scratch/stefan/7916156/working/building/REAL250005074556 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 678) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/678 `/scratch/stefan/7916156/working/3D/678' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)=CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F) `REAL250005074556.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074556/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074556 none CC(C)=CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 7, 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, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 58, 49, 49, 49, 26, 26, 26, 26, 10, 1, 10, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 58, 58, 58, 58, 58, 58, 58, 49, 26, 26, 1, 26, 26] 58 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: 151 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074556 none CC(C)=CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 7, 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, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 24, 6, 6, 6, 1, 1, 1, 1, 1, 1, 7, 7, 26, 25, 26, 26, 26, 1, 1, 1, 1, 24, 24, 24, 24, 24, 24, 24, 6, 1, 1, 26, 1, 1] 58 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 33]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074556 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074556 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074556/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074556 Building REAL250005074557 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074557' /scratch/stefan/7916156/working/building/REAL250005074557 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074557 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074557/0 /scratch/stefan/7916156/working/building/REAL250005074557 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 679) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/679 `/scratch/stefan/7916156/working/3D/679' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F) `REAL250005074557.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074557/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074557 none CCCCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 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, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [200, 196, 176, 68, 68, 68, 25, 25, 25, 25, 7, 1, 7, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 200, 201, 201, 201, 201, 197, 197, 176, 176, 68, 25, 25, 1, 25, 25] 201 rigid atoms, others: [35, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37]) total number of confs: 797 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074557 none CCCCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 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, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 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: [99, 53, 37, 6, 6, 6, 1, 1, 1, 1, 1, 1, 7, 7, 25, 25, 25, 25, 25, 1, 1, 1, 1, 99, 101, 101, 95, 97, 66, 66, 37, 37, 6, 1, 1, 25, 1, 1] 201 rigid atoms, others: [33, 34, 36, 37, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35]) total number of confs: 556 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074557 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074557 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074557/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074557 Building REAL250005074558 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074558' /scratch/stefan/7916156/working/building/REAL250005074558 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074558 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074558/0 /scratch/stefan/7916156/working/building/REAL250005074558 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 680) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/680 `/scratch/stefan/7916156/working/3D/680' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F) `REAL250005074558.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074558/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074558 none CC(C)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [77, 59, 77, 59, 59, 30, 30, 30, 30, 9, 1, 9, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 77, 77, 77, 77, 77, 77, 77, 59, 30, 30, 1, 30, 30] 77 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: 249 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074558 none CC(C)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [28, 5, 28, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 30, 30, 30, 30, 30, 1, 1, 1, 1, 28, 28, 28, 28, 28, 28, 28, 5, 1, 1, 30, 1, 1] 77 rigid atoms, others: [33, 34, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 32, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074558 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074558 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074558/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074558 Building REAL250005074559 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074559' /scratch/stefan/7916156/working/building/REAL250005074559 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074559 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074559/0 /scratch/stefan/7916156/working/building/REAL250005074559 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 681) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/681 `/scratch/stefan/7916156/working/3D/681' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F) `REAL250005074559.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074559/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074559 none CCC(C)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 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, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [108, 108, 58, 108, 58, 58, 24, 24, 24, 24, 10, 1, 10, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 108, 108, 108, 108, 108, 108, 108, 108, 108, 58, 24, 24, 1, 24, 24] 108 rigid atoms, others: [35, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37]) total number of confs: 375 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074559 none CCC(C)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 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, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [50, 42, 6, 42, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 24, 24, 24, 24, 24, 1, 1, 1, 1, 55, 55, 55, 55, 55, 42, 42, 42, 42, 6, 1, 1, 24, 1, 1] 108 rigid atoms, others: [33, 34, 36, 37, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35]) total number of confs: 277 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074559 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074559 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074559/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074559 Building REAL250005074560 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074560' /scratch/stefan/7916156/working/building/REAL250005074560 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074560 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074560/0 /scratch/stefan/7916156/working/building/REAL250005074560 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 682) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/682 `/scratch/stefan/7916156/working/3D/682' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F) `REAL250005074560.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074560/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074560 none C=CCCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 7, 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, 7, 7, 6, 7, 7, 7, 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, 173, 75, 75, 75, 24, 24, 24, 24, 8, 1, 8, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 201, 201, 201, 201, 201, 173, 173, 75, 24, 24, 1, 24, 24] 201 rigid atoms, others: [33, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35]) total number of confs: 763 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074560 none C=CCCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 7, 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, 7, 7, 6, 7, 7, 7, 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: [138, 82, 46, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 24, 24, 24, 24, 24, 1, 1, 1, 1, 138, 138, 138, 82, 82, 46, 46, 6, 1, 1, 24, 1, 1] 201 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 33]) total number of confs: 576 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074560 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074560 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074560/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074560 Building REAL250005074561 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074561' /scratch/stefan/7916156/working/building/REAL250005074561 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074561 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074561/0 /scratch/stefan/7916156/working/building/REAL250005074561 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 683) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/683 `/scratch/stefan/7916156/working/3D/683' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=C(C)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F) `REAL250005074561.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074561/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074561 none CC=C(C)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 7, 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, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 91 conformations in input total number of sets (complete confs): 91 using faster count positions algorithm for large data unique positions, atoms: [91, 91, 58, 91, 58, 58, 34, 34, 34, 34, 10, 1, 10, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 91, 91, 91, 91, 91, 91, 91, 58, 34, 34, 1, 34, 34] 91 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: 241 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074561 none CC=C(C)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 7, 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, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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: [36, 36, 5, 36, 5, 5, 1, 1, 1, 1, 1, 1, 6, 6, 34, 34, 34, 34, 34, 1, 1, 1, 1, 36, 36, 36, 36, 36, 36, 36, 5, 1, 1, 34, 1, 1] 91 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 33]) total number of confs: 127 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074561 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074561 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074561/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074561 Building REAL250005074562 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074562' /scratch/stefan/7916156/working/building/REAL250005074562 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074562 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074562/0 /scratch/stefan/7916156/working/building/REAL250005074562 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 684) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/684 `/scratch/stefan/7916156/working/3D/684' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C(=O)N[C@@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@@H]2F)CC1) `REAL250005074562.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074562/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074562 none CC1(C(=O)N[C@@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@@H]2F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 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: [29, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 26, 26, 26, 26, 26, 1, 1, 1, 1, 29, 29, 29, 29, 29, 6, 1, 1, 26, 1, 1, 29, 29, 29, 29] 80 rigid atoms, others: [4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 27, 28, 30, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 29, 32, 33, 34, 35]) total number of confs: 107 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074562 none CC1(C(=O)N[C@@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@@H]2F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 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: [1, 1, 1, 7, 7, 7, 29, 29, 29, 29, 64, 64, 80, 80, 80, 80, 80, 29, 29, 29, 29, 1, 1, 2, 2, 2, 7, 29, 29, 80, 29, 29, 1, 1, 1, 1] 80 rigid atoms, others: [0, 1, 2, 35, 33, 32, 34, 21, 22] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074562 none CC1(C(=O)N[C@@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@@H]2F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 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, 55, 55, 55, 26, 26, 26, 26, 8, 1, 8, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 80, 80, 80, 80, 80, 55, 26, 26, 1, 26, 26, 80, 80, 80, 80] 80 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: 227 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074562 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074562 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074562/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074562 Building REAL250005074563 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074563' /scratch/stefan/7916156/working/building/REAL250005074563 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074563 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074563/0 /scratch/stefan/7916156/working/building/REAL250005074563 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 685) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/685 `/scratch/stefan/7916156/working/3D/685' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H]1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F) `REAL250005074563.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074563.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074563/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074563 none C[C@@H]1C[C@H]1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [35, 35, 35, 35, 5, 35, 5, 5, 1, 1, 1, 1, 1, 1, 6, 6, 28, 28, 28, 28, 28, 1, 1, 1, 1, 35, 35, 35, 35, 35, 5, 1, 1, 28, 1, 1] 97 rigid atoms, others: [32, 34, 35, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 33]) total number of confs: 119 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074563 none C[C@@H]1C[C@H]1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 35, 35, 35, 35, 78, 78, 97, 97, 97, 97, 97, 35, 35, 35, 35, 2, 2, 2, 1, 1, 13, 35, 35, 97, 35, 35] 97 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35]) total number of confs: 260 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074563 none C[C@@H]1C[C@H]1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 58, 97, 58, 58, 28, 28, 28, 28, 9, 1, 9, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 97, 97, 97, 97, 97, 58, 28, 28, 1, 28, 28] 97 rigid atoms, others: [33, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35]) total number of confs: 274 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074563 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074563 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074563/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074563 Building REAL250005074564 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074564' /scratch/stefan/7916156/working/building/REAL250005074564 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074564 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074564/0 /scratch/stefan/7916156/working/building/REAL250005074564 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 686) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/686 `/scratch/stefan/7916156/working/3D/686' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@@H]1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F) `REAL250005074564.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074564.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074564/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074564 none C[C@H]1C[C@@H]1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 43, 43, 6, 43, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 22, 22, 22, 22, 22, 1, 1, 1, 1, 43, 43, 43, 43, 43, 6, 1, 1, 22, 1, 1] 79 rigid atoms, others: [32, 34, 35, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 33]) total number of confs: 130 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074564 none C[C@H]1C[C@@H]1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 43, 43, 43, 43, 76, 76, 79, 79, 79, 79, 79, 43, 43, 43, 43, 2, 2, 2, 1, 1, 13, 43, 43, 79, 43, 43] 79 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35]) total number of confs: 235 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.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: REAL250005074564 none C[C@H]1C[C@@H]1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [79, 79, 79, 79, 49, 79, 49, 49, 22, 22, 22, 22, 9, 1, 9, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 79, 79, 79, 79, 79, 49, 22, 22, 1, 22, 22] 79 rigid atoms, others: [33, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35]) total number of confs: 225 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074564 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074564 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074564/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074564 Building REAL250005074565 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074565' /scratch/stefan/7916156/working/building/REAL250005074565 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074565 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074565/0 /scratch/stefan/7916156/working/building/REAL250005074565 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 687) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/687 `/scratch/stefan/7916156/working/3D/687' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F) `REAL250005074565.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074565/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074565 none NC(=O)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 6, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [67, 52, 67, 52, 52, 31, 31, 31, 31, 10, 1, 10, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 67, 67, 52, 31, 31, 1, 31, 31] 67 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29]) total number of confs: 174 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074565 none NC(=O)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 6, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 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: [20, 5, 22, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 31, 31, 31, 31, 31, 1, 1, 1, 1, 20, 22, 5, 1, 1, 31, 1, 1] 67 rigid atoms, others: [5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 25, 26, 28, 29] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 27]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074565 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074565 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074565/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074565 Building REAL250005074566 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074566' /scratch/stefan/7916156/working/building/REAL250005074566 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074566 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074566/0 /scratch/stefan/7916156/working/building/REAL250005074566 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 688) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/688 `/scratch/stefan/7916156/working/3D/688' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F) `REAL250005074566.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074566/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074566 none CC(C)(C)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 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, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 42, 42, 42, 42, 20, 20, 20, 20, 10, 1, 10, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 20, 20, 1, 20, 20] 42 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: 110 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074566 none CC(C)(C)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 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, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 9, 9, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 20, 20, 20, 20, 20, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 1, 1, 20, 1, 1] 42 rigid atoms, others: [33, 34, 36, 37, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074566 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074566 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074566/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074566 Building REAL250005074567 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074567' /scratch/stefan/7916156/working/building/REAL250005074567 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074567 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074567/0 /scratch/stefan/7916156/working/building/REAL250005074567 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 689) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/689 `/scratch/stefan/7916156/working/3D/689' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F) `REAL250005074567.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074567/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074567 none C=CCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 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, 104, 58, 58, 58, 25, 25, 25, 25, 8, 1, 8, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 104, 104, 104, 104, 104, 58, 25, 25, 1, 25, 25] 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: 371 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074567 none C=CCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 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: [70, 43, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 25, 25, 25, 25, 25, 1, 1, 1, 1, 70, 70, 70, 43, 43, 6, 1, 1, 25, 1, 1] 104 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 28, 29, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 30]) total number of confs: 268 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074567 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074567 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074567/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074567 Building REAL250005074568 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074568' /scratch/stefan/7916156/working/building/REAL250005074568 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074568 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074568/0 /scratch/stefan/7916156/working/building/REAL250005074568 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 690) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/690 `/scratch/stefan/7916156/working/3D/690' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(O)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F) `REAL250005074568.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074568/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074568 none C=CC(O)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 276 conformations in input total number of sets (complete confs): 276 using faster count positions algorithm for large data unique positions, atoms: [92, 92, 53, 92, 53, 53, 26, 26, 26, 25, 8, 1, 8, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 92, 92, 92, 92, 276, 53, 25, 25, 1, 26, 26] 276 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33]) total number of confs: 591 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074568 none C=CC(O)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 276 conformations in input total number of sets (complete confs): 276 using faster count positions algorithm for large data unique positions, atoms: [53, 32, 5, 32, 5, 5, 1, 1, 1, 1, 1, 1, 6, 6, 25, 25, 25, 25, 25, 1, 1, 1, 1, 53, 53, 53, 32, 96, 5, 1, 1, 25, 1, 1] 276 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 31]) total number of confs: 303 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074568 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074568 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074568/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074568 Building REAL250005074569 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074569' /scratch/stefan/7916156/working/building/REAL250005074569 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074569 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074569/0 /scratch/stefan/7916156/working/building/REAL250005074569 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 691) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/691 `/scratch/stefan/7916156/working/3D/691' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F)C1COC1) `REAL250005074569.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074569.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074569/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074569 none O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F)C1COC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 5, 5, 12, 5, 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, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 3, 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: [46, 46, 25, 25, 25, 25, 9, 1, 9, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 46, 69, 69, 69, 46, 25, 25, 1, 25, 25, 69, 69, 69, 69, 69] 69 rigid atoms, others: [7, 9, 10, 11, 12, 13, 14, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 191 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074569 none O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F)C1COC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 5, 5, 12, 5, 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, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 3, 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: [6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 25, 25, 25, 25, 25, 1, 1, 1, 1, 6, 40, 40, 40, 6, 1, 1, 25, 1, 1, 40, 40, 40, 40, 40] 69 rigid atoms, others: [2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 24, 25, 27, 28] set([0, 1, 33, 32, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 26, 29, 30, 31]) total number of confs: 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.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: REAL250005074569 none O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F)C1COC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 5, 5, 12, 5, 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, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 3, 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: [11, 1, 11, 11, 40, 40, 40, 40, 65, 65, 69, 69, 69, 69, 69, 40, 40, 40, 40, 1, 1, 1, 1, 11, 40, 40, 69, 40, 40, 1, 1, 1, 1, 1] 69 rigid atoms, others: [32, 1, 33, 19, 20, 21, 22, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28]) total number of confs: 201 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074569 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074569 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074569/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074569 Building REAL250005074570 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074570' /scratch/stefan/7916156/working/building/REAL250005074570 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074570 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074570/0 /scratch/stefan/7916156/working/building/REAL250005074570 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 692) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/692 `/scratch/stefan/7916156/working/3D/692' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC=CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F) `REAL250005074570.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074570.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074570/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074570 none CCC=CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 7, 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, 7, 7, 6, 7, 7, 7, 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, 94, 94, 63, 63, 63, 26, 26, 26, 26, 8, 1, 8, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 118, 118, 118, 118, 118, 94, 94, 63, 26, 26, 1, 26, 26] 118 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: 420 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074570 none CCC=CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 7, 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, 7, 7, 6, 7, 7, 7, 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: [65, 36, 36, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 26, 26, 26, 26, 26, 1, 1, 1, 1, 65, 65, 65, 65, 65, 36, 36, 6, 1, 1, 26, 1, 1] 118 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 33]) total number of confs: 277 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074570 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074570 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074570/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074570 Building REAL250005074571 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074571' /scratch/stefan/7916156/working/building/REAL250005074571 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types Protomer extracton resulted in 0 protomers Marking REAL250005074571 as failed and skipping /scratch/stefan/7916156/working /scratch/stefan/7916156 `/scratch/stefan/7916156/working/building/REAL250005074571' -> `/scratch/stefan/7916156/failed/REAL250005074571' Building REAL250005074572 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074572' /scratch/stefan/7916156/working/building/REAL250005074572 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074572 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074572/0 /scratch/stefan/7916156/working/building/REAL250005074572 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 693) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/693 `/scratch/stefan/7916156/working/3D/693' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CO)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F) `REAL250005074572.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074572.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074572/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074572 none O=C(CO)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [40, 40, 40, 41, 23, 23, 23, 23, 9, 1, 9, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 41, 41, 123, 40, 23, 23, 1, 23, 23] 123 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29]) total number of confs: 222 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074572 none O=C(CO)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 26, 1, 1, 1, 1, 1, 1, 6, 6, 23, 23, 23, 23, 23, 1, 1, 1, 1, 26, 26, 78, 6, 1, 1, 23, 1, 1] 123 rigid atoms, others: [4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 25, 26, 28, 29] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 27]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074572 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074572 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074572/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074572 Building REAL250005074573 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074573' /scratch/stefan/7916156/working/building/REAL250005074573 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074573 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074573/0 /scratch/stefan/7916156/working/building/REAL250005074573 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 694) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/694 `/scratch/stefan/7916156/working/3D/694' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F) `REAL250005074573.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074573/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074573 none CC(O)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 65, 88, 65, 65, 32, 32, 32, 32, 9, 1, 9, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 88, 88, 88, 88, 264, 65, 32, 32, 1, 32, 32] 264 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: 542 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074573 none CC(O)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [36, 6, 36, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 32, 32, 32, 32, 32, 1, 1, 1, 1, 36, 36, 36, 36, 108, 6, 1, 1, 32, 1, 1] 264 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 28, 29, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 30]) total number of confs: 270 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074573 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074573 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074573/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074573 Building REAL250005074574 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074574' /scratch/stefan/7916156/working/building/REAL250005074574 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074574 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074574/0 /scratch/stefan/7916156/working/building/REAL250005074574 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 695) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/695 `/scratch/stefan/7916156/working/3D/695' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCF)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F) `REAL250005074574.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074574/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074574 none O=C(CCF)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 15, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 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: [61, 61, 61, 140, 140, 25, 25, 25, 25, 7, 1, 7, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 140, 140, 140, 140, 61, 25, 25, 1, 25, 25] 140 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]) total number of confs: 515 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074574 none O=C(CCF)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 15, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 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: [5, 5, 5, 34, 65, 1, 1, 1, 1, 1, 1, 7, 7, 25, 25, 25, 25, 25, 1, 1, 1, 1, 34, 34, 65, 65, 5, 1, 1, 25, 1, 1] 140 rigid atoms, others: [5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 27, 28, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 29]) total number of confs: 298 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074574 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074574 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074574/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074574 Building REAL250005074575 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074575' /scratch/stefan/7916156/working/building/REAL250005074575 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074575 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074575/0 /scratch/stefan/7916156/working/building/REAL250005074575 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 696) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/696 `/scratch/stefan/7916156/working/3D/696' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F) `REAL250005074575.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074575.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074575/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074575 none C#CCCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 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, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 177 conformations in input total number of sets (complete confs): 177 using faster count positions algorithm for large data unique positions, atoms: [177, 177, 167, 74, 74, 74, 31, 31, 31, 31, 8, 1, 8, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 177, 177, 177, 167, 167, 74, 31, 31, 1, 31, 31] 177 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33]) total number of confs: 642 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074575 none C#CCCC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 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, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 177 conformations in input total number of sets (complete confs): 177 using faster count positions algorithm for large data unique positions, atoms: [69, 69, 34, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 31, 31, 31, 31, 31, 1, 1, 1, 1, 69, 69, 69, 34, 34, 5, 1, 1, 31, 1, 1] 177 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 31]) total number of confs: 334 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074575 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074575 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074575/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074575 Building REAL250005074576 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074576' /scratch/stefan/7916156/working/building/REAL250005074576 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074576 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074576/0 /scratch/stefan/7916156/working/building/REAL250005074576 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 697) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/697 `/scratch/stefan/7916156/working/3D/697' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F)C1CCO1) `REAL250005074576.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074576/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074576 none O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F)C1CCO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 5, 5, 5, 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, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 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: [38, 38, 18, 18, 18, 18, 10, 1, 10, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 38, 53, 53, 53, 38, 18, 18, 1, 18, 18, 53, 53, 53, 53, 53] 53 rigid atoms, others: [7, 9, 10, 11, 12, 13, 14, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 142 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074576 none O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F)C1CCO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 5, 5, 5, 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, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 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: [6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 18, 18, 18, 18, 18, 1, 1, 1, 1, 6, 29, 29, 29, 6, 1, 1, 18, 1, 1, 29, 29, 29, 29, 29] 53 rigid atoms, others: [2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 24, 25, 27, 28] set([0, 1, 33, 32, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 26, 29, 30, 31]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074576 none O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F)C1CCO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 5, 5, 5, 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, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 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: [11, 1, 11, 11, 29, 29, 29, 29, 44, 44, 53, 53, 53, 53, 53, 29, 29, 29, 29, 1, 1, 1, 1, 11, 29, 29, 53, 29, 29, 1, 1, 1, 1, 1] 53 rigid atoms, others: [32, 1, 33, 19, 20, 21, 22, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28]) total number of confs: 144 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074576 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074576 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074576/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074576 Building REAL250005074577 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074577' /scratch/stefan/7916156/working/building/REAL250005074577 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074577 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074577/0 /scratch/stefan/7916156/working/building/REAL250005074577 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 698) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/698 `/scratch/stefan/7916156/working/3D/698' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F) `REAL250005074577.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074577/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074577 none CC1=CC1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 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, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 115 conformations in input total number of sets (complete confs): 115 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 41, 5, 5, 5, 1, 1, 1, 1, 1, 1, 6, 6, 27, 27, 27, 27, 27, 1, 1, 1, 1, 41, 41, 41, 41, 41, 5, 1, 1, 27, 1, 1] 115 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 31]) total number of confs: 130 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074577 none CC1=CC1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 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, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 115 conformations in input total number of sets (complete confs): 115 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 13, 13, 13, 41, 41, 41, 41, 91, 91, 115, 115, 115, 115, 115, 41, 41, 41, 41, 2, 2, 2, 1, 1, 13, 41, 41, 115, 41, 41] 115 rigid atoms, others: [0, 1, 2, 3, 4, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33]) 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.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: REAL250005074577 none CC1=CC1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 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, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 115 conformations in input total number of sets (complete confs): 115 using faster count positions algorithm for large data unique positions, atoms: [115, 115, 115, 49, 49, 49, 27, 27, 27, 27, 10, 1, 10, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 115, 115, 115, 115, 115, 49, 27, 27, 1, 27, 27] 115 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33]) total number of confs: 312 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074577 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074577 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074577/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074577 Building REAL250005074578 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074578' /scratch/stefan/7916156/working/building/REAL250005074578 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074578 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074578/0 /scratch/stefan/7916156/working/building/REAL250005074578 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 699) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/699 `/scratch/stefan/7916156/working/3D/699' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F) `REAL250005074578.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074578/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074578 none C[C@@H](O)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 273 conformations in input total number of sets (complete confs): 273 using faster count positions algorithm for large data unique positions, atoms: [91, 71, 91, 91, 71, 71, 32, 32, 32, 32, 10, 1, 10, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 91, 91, 91, 273, 71, 32, 32, 1, 32, 32] 273 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32]) total number of confs: 566 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074578 none C[C@@H](O)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 273 conformations in input total number of sets (complete confs): 273 using faster count positions algorithm for large data unique positions, atoms: [42, 6, 42, 42, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 32, 32, 32, 32, 32, 1, 1, 1, 1, 42, 42, 42, 126, 6, 1, 1, 32, 1, 1] 273 rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 28, 29, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 30]) total number of confs: 306 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074578 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074578 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074578/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074578 Building REAL250005074579 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074579' /scratch/stefan/7916156/working/building/REAL250005074579 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074579 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074579/0 /scratch/stefan/7916156/working/building/REAL250005074579 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 700) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/700 `/scratch/stefan/7916156/working/3D/700' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(C=CCO)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F) `REAL250005074579.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074579.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074579/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074579 none O=C(C=CCO)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 5, 12, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 4, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 342 conformations in input total number of sets (complete confs): 342 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 65, 112, 112, 114, 24, 24, 24, 24, 10, 1, 10, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 112, 112, 114, 114, 342, 65, 24, 24, 1, 24, 24] 342 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33]) total number of confs: 672 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074579 none O=C(C=CCO)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 5, 12, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 4, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 342 conformations in input total number of sets (complete confs): 342 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 31, 31, 68, 1, 1, 1, 1, 1, 1, 6, 6, 24, 24, 24, 24, 24, 1, 1, 1, 1, 31, 31, 68, 68, 204, 6, 1, 1, 24, 1, 1] 342 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 31]) total number of confs: 474 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074579 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074579 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074579/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074579 Building REAL250005074580 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074580' /scratch/stefan/7916156/working/building/REAL250005074580 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074580 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074580/0 /scratch/stefan/7916156/working/building/REAL250005074580 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 701) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/701 `/scratch/stefan/7916156/working/3D/701' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F)C1=CCC1) `REAL250005074580.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074580/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074580 none O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F)C1=CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 1, 1, 5, 5, 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, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 17, 17, 17, 17, 8, 1, 8, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 28, 28, 28, 28, 28, 17, 17, 1, 17, 17, 28, 28, 28, 28, 28] 28 rigid atoms, others: [7, 9, 10, 11, 12, 13, 14, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 72 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074580 none O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F)C1=CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 1, 1, 5, 5, 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, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 17, 17, 17, 17, 17, 1, 1, 1, 1, 5, 11, 11, 11, 5, 1, 1, 17, 1, 1, 11, 11, 11, 11, 11] 28 rigid atoms, others: [2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 24, 25, 27, 28] set([0, 1, 33, 32, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 26, 29, 30, 31]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074580 none O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F)C1=CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 1, 1, 5, 5, 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, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 11, 11, 11, 11, 22, 22, 28, 28, 28, 28, 28, 11, 11, 11, 11, 1, 1, 1, 1, 6, 11, 11, 28, 11, 11, 1, 1, 1, 1, 1] 28 rigid atoms, others: [32, 1, 33, 19, 20, 21, 22, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28]) total number of confs: 70 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074580 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074580 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074580/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074580 Building REAL250005074581 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074581' /scratch/stefan/7916156/working/building/REAL250005074581 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074581 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074581/0 /scratch/stefan/7916156/working/building/REAL250005074581 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 702) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/702 `/scratch/stefan/7916156/working/3D/702' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F) `REAL250005074581.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074581/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074581 none C[C@H](O)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 186 conformations in input total number of sets (complete confs): 186 using faster count positions algorithm for large data unique positions, atoms: [62, 48, 62, 62, 48, 48, 27, 27, 27, 27, 10, 1, 10, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 62, 62, 62, 186, 48, 27, 27, 1, 27, 27] 186 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32]) total number of confs: 375 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074581 none C[C@H](O)C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 186 conformations in input total number of sets (complete confs): 186 using faster count positions algorithm for large data unique positions, atoms: [32, 6, 32, 32, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 27, 27, 27, 27, 27, 1, 1, 1, 1, 32, 32, 32, 96, 6, 1, 1, 27, 1, 1] 186 rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 28, 29, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 30]) total number of confs: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074581 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074581 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074581/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074581 Building REAL250005074582 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074582' /scratch/stefan/7916156/working/building/REAL250005074582 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074582 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074582/0 /scratch/stefan/7916156/working/building/REAL250005074582 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 703) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/703 `/scratch/stefan/7916156/working/3D/703' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C1CC1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F) `REAL250005074582.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074582/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074582 none C=C1CC1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 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, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 92 conformations in input total number of sets (complete confs): 92 using faster count positions algorithm for large data unique positions, atoms: [47, 47, 47, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 25, 25, 25, 25, 25, 1, 1, 1, 1, 47, 47, 47, 47, 47, 6, 1, 1, 25, 1, 1] 92 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 31]) total number of confs: 142 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074582 none C=C1CC1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 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, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 92 conformations in input total number of sets (complete confs): 92 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 13, 13, 13, 47, 47, 47, 47, 81, 81, 92, 92, 92, 92, 92, 47, 47, 47, 47, 1, 1, 1, 1, 1, 13, 47, 47, 92, 47, 47] 92 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 25, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33]) 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.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: REAL250005074582 none C=C1CC1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 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, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 53, 53, 53, 25, 25, 25, 25, 10, 1, 10, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 92, 92, 92, 92, 92, 53, 25, 25, 1, 25, 25] 92 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33]) total number of confs: 258 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074582 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074582 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074582/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074582 Building REAL250005074583 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074583' /scratch/stefan/7916156/working/building/REAL250005074583 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074583 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074583/0 /scratch/stefan/7916156/working/building/REAL250005074583 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 704) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/704 `/scratch/stefan/7916156/working/3D/704' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F) `REAL250005074583.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074583/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074583 none C=C(C)CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 7, 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, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 122 conformations in input total number of sets (complete confs): 122 using faster count positions algorithm for large data unique positions, atoms: [122, 122, 122, 70, 70, 70, 26, 26, 26, 26, 10, 1, 10, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 122, 122, 122, 122, 122, 122, 122, 70, 26, 26, 1, 26, 26] 122 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: 419 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074583 none C=C(C)CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 7, 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, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 122 conformations in input total number of sets (complete confs): 122 using faster count positions algorithm for large data unique positions, atoms: [68, 48, 68, 6, 6, 6, 1, 1, 1, 1, 1, 1, 7, 7, 26, 26, 26, 26, 26, 1, 1, 1, 1, 68, 68, 68, 68, 68, 48, 48, 6, 1, 1, 26, 1, 1] 122 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 33]) total number of confs: 264 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074583 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074583 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074583/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074583 Building REAL250005074584 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074584' /scratch/stefan/7916156/working/building/REAL250005074584 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074584 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074584/0 /scratch/stefan/7916156/working/building/REAL250005074584 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 705) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/705 `/scratch/stefan/7916156/working/3D/705' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F) `REAL250005074584.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074584/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074584 none CC=CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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, 43, 43, 43, 24, 24, 24, 24, 9, 1, 9, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 46, 46, 46, 46, 46, 43, 24, 24, 1, 24, 24] 46 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: 111 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074584 none CC=CC(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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: [26, 26, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 24, 24, 24, 24, 24, 1, 1, 1, 1, 26, 26, 26, 26, 26, 6, 1, 1, 24, 1, 1] 46 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 28, 29, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 30]) total number of confs: 98 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074584 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074584 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074584/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074584 Building REAL250005074585 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074585' /scratch/stefan/7916156/working/building/REAL250005074585 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074585 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074585/0 /scratch/stefan/7916156/working/building/REAL250005074585 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 706) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/706 `/scratch/stefan/7916156/working/3D/706' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H]1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F) `REAL250005074585.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074585/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074585 none C[C@@H]1C[C@H]1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [35, 35, 35, 35, 5, 35, 5, 5, 1, 1, 1, 1, 1, 1, 6, 6, 28, 28, 28, 28, 28, 1, 1, 1, 1, 35, 35, 35, 35, 35, 5, 1, 1, 28, 1, 1] 97 rigid atoms, others: [32, 34, 35, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 33]) total number of confs: 119 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074585 none C[C@@H]1C[C@H]1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 35, 35, 35, 35, 78, 78, 97, 97, 97, 97, 97, 35, 35, 35, 35, 2, 2, 2, 1, 1, 13, 35, 35, 97, 35, 35] 97 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35]) total number of confs: 260 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074585 none C[C@@H]1C[C@H]1C(=O)N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 58, 97, 58, 58, 28, 28, 28, 28, 9, 1, 9, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 97, 97, 97, 97, 97, 58, 28, 28, 1, 28, 28] 97 rigid atoms, others: [33, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35]) total number of confs: 274 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074585 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074585 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074585/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074585 Building REAL250005074586 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074586' /scratch/stefan/7916156/working/building/REAL250005074586 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074586 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074586/0 /scratch/stefan/7916156/working/building/REAL250005074586 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 707) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/707 `/scratch/stefan/7916156/working/3D/707' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F)C1(O)CC1) `REAL250005074586.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074586.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074586/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074586 none O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F)C1(O)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 5, 12, 5, 5, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 192 conformations in input total number of sets (complete confs): 192 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 23, 23, 23, 23, 9, 1, 9, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 49, 64, 64, 64, 49, 23, 23, 1, 23, 23, 192, 64, 64, 64, 64] 192 rigid atoms, others: [7, 9, 10, 11, 12, 13, 14, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 360 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074586 none O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F)C1(O)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 5, 12, 5, 5, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 192 conformations in input total number of sets (complete confs): 192 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 23, 23, 23, 23, 23, 1, 1, 1, 1, 6, 34, 34, 34, 6, 1, 1, 23, 1, 1, 102, 34, 34, 34, 34] 192 rigid atoms, others: [2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 24, 25, 27, 28] set([0, 1, 33, 32, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 26, 29, 30, 31]) total number of confs: 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.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: REAL250005074586 none O=C(N[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1F)C1(O)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 15, 5, 12, 5, 5, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 192 conformations in input total number of sets (complete confs): 192 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 34, 34, 34, 34, 61, 61, 64, 64, 64, 64, 64, 34, 34, 34, 34, 1, 1, 1, 1, 11, 34, 34, 64, 34, 34, 6, 1, 1, 1, 1] 192 rigid atoms, others: [32, 1, 33, 19, 20, 21, 22, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 193 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074586 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074586 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074586/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074586 Building REAL250005074587 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074587' /scratch/stefan/7916156/working/building/REAL250005074587 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074587 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074587/0 /scratch/stefan/7916156/working/building/REAL250005074587 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 708) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/708 `/scratch/stefan/7916156/working/3D/708' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1CC1)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1) `REAL250005074587.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074587/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074587 none O=C(CC1CC1)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 15, 5, 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 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 30, 40, 40, 1, 1, 1, 1, 1, 6, 6, 6, 20, 20, 20, 20, 20, 1, 1, 1, 1, 30, 30, 40, 40, 40, 40, 40, 1, 1, 6, 20, 1, 1] 76 rigid atoms, others: [1, 34, 35, 6, 7, 8, 9, 10, 19, 20, 21, 22, 30, 31] set([0, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 32, 33]) total number of confs: 172 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074587 none O=C(CC1CC1)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 15, 5, 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 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [15, 3, 1, 1, 1, 1, 15, 40, 40, 40, 40, 70, 70, 70, 76, 76, 76, 76, 76, 40, 40, 40, 40, 3, 3, 1, 1, 1, 1, 1, 40, 40, 70, 76, 40, 40] 76 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]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.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: REAL250005074587 none O=C(CC1CC1)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 15, 5, 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 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [44, 20, 44, 71, 76, 76, 20, 20, 8, 20, 8, 1, 8, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 71, 71, 76, 76, 76, 76, 76, 20, 20, 8, 1, 20, 20] 76 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: 278 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074587 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074587 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074587/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074587 Building REAL250005074588 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074588' /scratch/stefan/7916156/working/building/REAL250005074588 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074588 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074588/0 /scratch/stefan/7916156/working/building/REAL250005074588 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 709) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/709 `/scratch/stefan/7916156/working/3D/709' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1) `REAL250005074588.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074588.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074588/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074588 none COCC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 15, 5, 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 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [42, 40, 27, 15, 27, 15, 15, 6, 15, 6, 1, 6, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 42, 42, 42, 40, 40, 15, 15, 6, 1, 15, 15] 42 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: 142 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074588 none COCC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 15, 5, 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 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [31, 18, 5, 1, 5, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 15, 15, 15, 1, 1, 1, 1, 31, 31, 31, 18, 18, 1, 1, 5, 15, 1, 1] 42 rigid atoms, others: [32, 3, 5, 6, 7, 8, 9, 18, 19, 20, 21, 27, 28, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 29, 30]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074588 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074588 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074588/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074588 Building REAL250005074589 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074589' /scratch/stefan/7916156/working/building/REAL250005074589 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074589 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074589/0 /scratch/stefan/7916156/working/building/REAL250005074589 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 710) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/710 `/scratch/stefan/7916156/working/3D/710' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1) `REAL250005074589.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074589/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074589 none CCCC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [62, 60, 35, 18, 35, 18, 18, 9, 18, 9, 1, 9, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 62, 62, 62, 62, 62, 60, 60, 18, 18, 9, 1, 18, 18] 62 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: 218 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074589 none CCCC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [34, 26, 6, 1, 6, 1, 1, 1, 1, 1, 6, 6, 6, 18, 18, 18, 18, 18, 1, 1, 1, 1, 37, 37, 37, 36, 36, 27, 27, 1, 1, 6, 18, 1, 1] 62 rigid atoms, others: [33, 34, 3, 5, 6, 7, 8, 9, 18, 19, 20, 21, 29, 30] set([0, 1, 2, 4, 32, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 31]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074589 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074589 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074589/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074589 Building REAL250005074590 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074590' /scratch/stefan/7916156/working/building/REAL250005074590 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074590 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074590/0 /scratch/stefan/7916156/working/building/REAL250005074590 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 711) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/711 `/scratch/stefan/7916156/working/3D/711' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1) `REAL250005074590.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074590/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074590 none CC(C)CC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', '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, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 15, 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, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 26, 12, 26, 12, 12, 7, 12, 7, 1, 7, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 39, 39, 39, 39, 39, 39, 39, 39, 39, 12, 12, 8, 1, 12, 12] 39 rigid atoms, others: [35, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37]) total number of confs: 140 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074590 none CC(C)CC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', '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, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 15, 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, 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: [18, 18, 20, 6, 1, 6, 1, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 18, 18, 1, 1, 6, 12, 1, 1] 39 rigid atoms, others: [32, 33, 4, 37, 6, 7, 8, 9, 10, 19, 20, 21, 22, 36] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074590 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074590 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074590/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074590 Building REAL250005074591 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074591' /scratch/stefan/7916156/working/building/REAL250005074591 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074591 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074591/0 /scratch/stefan/7916156/working/building/REAL250005074591 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 712) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/712 `/scratch/stefan/7916156/working/3D/712' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC1C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1) `REAL250005074591.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074591/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074591 none CC1CC1C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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, 4, 1, 4, 1, 1, 1, 1, 1, 6, 6, 6, 13, 13, 13, 13, 13, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 1, 1, 6, 13, 1, 1] 30 rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 10, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 32, 33]) total number of confs: 58 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074591 none CC1CC1C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 6, 6, 14, 14, 14, 14, 27, 27, 27, 30, 30, 30, 30, 30, 14, 14, 14, 14, 2, 2, 2, 1, 1, 1, 1, 14, 14, 27, 30, 14, 14] 30 rigid atoms, others: [0, 1, 2, 3, 4, 26, 27, 28, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074591 none CC1CC1C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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, 18, 13, 18, 13, 13, 7, 13, 7, 1, 7, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 30, 30, 30, 30, 30, 30, 30, 13, 13, 7, 1, 13, 13] 30 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: 89 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074591 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074591 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074591/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074591 Building REAL250005074592 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074592' /scratch/stefan/7916156/working/building/REAL250005074592 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074592 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074592/0 /scratch/stefan/7916156/working/building/REAL250005074592 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 713) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/713 `/scratch/stefan/7916156/working/3D/713' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)=CC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1) `REAL250005074592.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074592/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074592 none CC(C)=CC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 25, 13, 25, 13, 13, 7, 13, 7, 1, 7, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 38, 38, 38, 38, 38, 38, 38, 13, 13, 7, 1, 13, 13] 38 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: 121 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074592 none CC(C)=CC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 6, 1, 6, 1, 1, 1, 1, 1, 6, 6, 6, 13, 13, 13, 13, 13, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 1, 1, 6, 13, 1, 1] 38 rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 10, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 32, 33]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074592 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074592 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074592/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074592 Building REAL250005074593 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074593' /scratch/stefan/7916156/working/building/REAL250005074593 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074593 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074593/0 /scratch/stefan/7916156/working/building/REAL250005074593 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 714) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/714 `/scratch/stefan/7916156/working/3D/714' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1) `REAL250005074593.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074593/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074593 none CCCCC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', '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, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 15, 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, 7, 7, 7] 0 hydrogens need rotated 133 conformations in input total number of sets (complete confs): 133 using faster count positions algorithm for large data unique positions, atoms: [133, 124, 111, 52, 24, 52, 24, 24, 10, 24, 10, 1, 10, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 133, 133, 133, 133, 133, 124, 124, 111, 111, 24, 24, 10, 1, 24, 24] 133 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: 533 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074593 none CCCCC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', '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, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 15, 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, 7, 7, 7] 0 hydrogens need rotated 133 conformations in input total number of sets (complete confs): 133 using faster count positions algorithm for large data unique positions, atoms: [77, 47, 34, 7, 1, 7, 1, 1, 1, 1, 1, 5, 5, 5, 24, 24, 24, 24, 24, 1, 1, 1, 1, 77, 77, 77, 74, 74, 53, 53, 34, 34, 1, 1, 5, 24, 1, 1] 133 rigid atoms, others: [32, 33, 4, 37, 6, 7, 8, 9, 10, 19, 20, 21, 22, 36] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35]) total number of confs: 391 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074593 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074593 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074593/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074593 Building REAL250005074594 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074594' /scratch/stefan/7916156/working/building/REAL250005074594 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074594 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074594/0 /scratch/stefan/7916156/working/building/REAL250005074594 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 715) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/715 `/scratch/stefan/7916156/working/3D/715' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1) `REAL250005074594.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074594/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074594 none CC(C)C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 14, 21, 14, 14, 9, 14, 8, 1, 8, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 21, 21, 21, 21, 21, 21, 21, 14, 14, 9, 1, 14, 14] 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: 57 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074594 none CC(C)C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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: [9, 6, 9, 1, 6, 1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 14, 14, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 1, 1, 6, 14, 1, 1] 21 rigid atoms, others: [33, 34, 3, 5, 6, 7, 8, 9, 18, 19, 20, 21, 29, 30] set([0, 1, 2, 4, 32, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 31]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074594 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074594 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074594/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074594 Building REAL250005074595 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074595' /scratch/stefan/7916156/working/building/REAL250005074595 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074595 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074595/0 /scratch/stefan/7916156/working/building/REAL250005074595 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 716) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/716 `/scratch/stefan/7916156/working/3D/716' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1) `REAL250005074595.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074595/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074595 none CCC(C)C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', '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, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 15, 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, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [40, 39, 33, 39, 16, 33, 16, 16, 8, 16, 8, 1, 8, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 40, 40, 40, 40, 40, 39, 39, 39, 39, 16, 16, 8, 1, 16, 16] 40 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: 131 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074595 none CCC(C)C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', '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, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 15, 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, 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: [19, 15, 6, 15, 1, 6, 1, 1, 1, 1, 1, 6, 6, 6, 16, 16, 16, 16, 16, 1, 1, 1, 1, 19, 19, 19, 19, 19, 15, 15, 15, 15, 1, 1, 6, 16, 1, 1] 40 rigid atoms, others: [32, 33, 4, 37, 6, 7, 8, 9, 10, 19, 20, 21, 22, 36] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074595 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074595 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074595/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074595 Building REAL250005074596 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074596' /scratch/stefan/7916156/working/building/REAL250005074596 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074596 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074596/0 /scratch/stefan/7916156/working/building/REAL250005074596 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 717) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/717 `/scratch/stefan/7916156/working/3D/717' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1) `REAL250005074596.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074596/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074596 none C=CCCC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 126 conformations in input total number of sets (complete confs): 126 using faster count positions algorithm for large data unique positions, atoms: [126, 126, 104, 42, 18, 42, 18, 18, 8, 18, 8, 1, 8, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 126, 126, 126, 126, 126, 104, 104, 18, 18, 8, 1, 18, 18] 126 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: 513 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074596 none C=CCCC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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: [88, 51, 32, 7, 1, 7, 1, 1, 1, 1, 1, 5, 5, 5, 18, 18, 18, 18, 18, 1, 1, 1, 1, 88, 88, 88, 51, 51, 32, 32, 1, 1, 5, 18, 1, 1] 126 rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 10, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 32, 33]) total number of confs: 363 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074596 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074596 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074596/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074596 Building REAL250005074597 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074597' /scratch/stefan/7916156/working/building/REAL250005074597 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074597 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074597/0 /scratch/stefan/7916156/working/building/REAL250005074597 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 718) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/718 `/scratch/stefan/7916156/working/3D/718' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C#N)C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1) `REAL250005074597.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074597/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074597 none CC(C#N)C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.1', 'N.1', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 15, 5, 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] 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, 26, 30, 30, 15, 26, 15, 15, 7, 15, 7, 1, 7, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 30, 30, 30, 30, 15, 15, 7, 1, 15, 15] 30 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32]) total number of confs: 94 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074597 none CC(C#N)C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.1', 'N.1', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 15, 5, 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] 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: [18, 7, 18, 18, 1, 7, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 15, 15, 15, 1, 1, 1, 1, 18, 18, 18, 18, 1, 1, 5, 15, 1, 1] 30 rigid atoms, others: [32, 4, 6, 7, 8, 9, 10, 19, 20, 21, 22, 27, 28, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 29, 30]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074597 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074597 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074597/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074597 Building REAL250005074598 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074598' /scratch/stefan/7916156/working/building/REAL250005074598 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074598 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074598/0 /scratch/stefan/7916156/working/building/REAL250005074598 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 719) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/719 `/scratch/stefan/7916156/working/3D/719' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=C(C)C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1) `REAL250005074598.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074598.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074598/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074598 none CC=C(C)C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 29, 43, 14, 29, 14, 14, 7, 14, 7, 1, 7, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 43, 43, 43, 43, 43, 43, 43, 14, 14, 7, 1, 14, 14] 43 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: 135 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074598 none CC=C(C)C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 7, 22, 1, 7, 1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 14, 14, 1, 1, 1, 1, 22, 22, 22, 22, 22, 22, 22, 1, 1, 6, 14, 1, 1] 43 rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 10, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 32, 33]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074598 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074598 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074598/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074598 Building REAL250005074599 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074599' /scratch/stefan/7916156/working/building/REAL250005074599 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074599 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074599/0 /scratch/stefan/7916156/working/building/REAL250005074599 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 720) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/720 `/scratch/stefan/7916156/working/3D/720' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1) `REAL250005074599.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074599.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074599/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074599 none CCC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 15, 5, 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 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [26, 25, 18, 25, 18, 18, 11, 18, 11, 1, 11, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 26, 26, 26, 26, 26, 18, 18, 11, 1, 18, 18] 26 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: 77 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074599 none CCC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 15, 5, 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 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 1, 6, 1, 1, 1, 1, 1, 5, 5, 5, 18, 18, 18, 18, 18, 1, 1, 1, 1, 11, 11, 11, 10, 10, 1, 1, 5, 18, 1, 1] 26 rigid atoms, others: [2, 4, 5, 6, 7, 8, 17, 18, 19, 20, 26, 27, 30, 31] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 28, 29]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074599 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074599 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074599/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074599 Building REAL250005074600 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074600' /scratch/stefan/7916156/working/building/REAL250005074600 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074600 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074600/0 /scratch/stefan/7916156/working/building/REAL250005074600 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 721) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/721 `/scratch/stefan/7916156/working/3D/721' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1) `REAL250005074600.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074600/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074600 none CC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 15, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 10, 13, 10, 10, 7, 10, 7, 1, 7, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 13, 13, 13, 10, 10, 7, 1, 10, 10] 13 rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28]) total number of confs: 37 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074600 none CC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 15, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 5, 5, 5, 10, 10, 10, 10, 10, 1, 1, 1, 1, 3, 3, 3, 1, 1, 5, 10, 1, 1] 13 rigid atoms, others: [1, 3, 4, 5, 6, 7, 16, 17, 18, 19, 23, 24, 27, 28] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 25, 26]) total number of confs: 29 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074600 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074600 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074600/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074600 Building REAL250005074601 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074601' /scratch/stefan/7916156/working/building/REAL250005074601 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074601 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074601/0 /scratch/stefan/7916156/working/building/REAL250005074601 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 722) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/722 `/scratch/stefan/7916156/working/3D/722' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CN(C(=O)C2CC2)C[C@@H]1F)C1=CC(=O)[N-]O1) `REAL250005074601.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074601/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074601 none O=C(N[C@@H]1CN(C(=O)C2CC2)C[C@@H]1F)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'F', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 16, 16, 16, 16, 8, 1, 8, 1, 1, 1, 16, 16, 16, 16, 22, 24, 24, 24, 24, 24, 22, 16, 16, 1, 1, 1, 1, 1, 16, 16, 24] 24 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: 53 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074601 none O=C(N[C@@H]1CN(C(=O)C2CC2)C[C@@H]1F)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'F', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 1, 5, 5, 16, 16, 1, 1, 1, 1, 6, 12, 12, 12, 12, 12, 6, 1, 1, 16, 16, 16, 16, 16, 1, 1, 12] 24 rigid atoms, others: [2, 3, 4, 5, 6, 7, 12, 13, 14, 15, 23, 24, 30, 31] set([0, 1, 32, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29]) 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.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: REAL250005074601 none O=C(N[C@@H]1CN(C(=O)C2CC2)C[C@@H]1F)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'F', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 7, 12, 12, 12, 12, 17, 17, 24, 24, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 7, 12, 12, 24, 24, 24, 24, 24, 12, 12, 1] 24 rigid atoms, others: [32, 1, 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]) total number of confs: 73 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074601 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074601 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074601/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074601 Building REAL250005074602 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074602' /scratch/stefan/7916156/working/building/REAL250005074602 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074602 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074602/0 /scratch/stefan/7916156/working/building/REAL250005074602 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 723) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/723 `/scratch/stefan/7916156/working/3D/723' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CN(C(=O)C2CCC2)C[C@@H]1F)C1=CC(=O)[N-]O1) `REAL250005074602.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074602/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074602 none O=C(N[C@@H]1CN(C(=O)C2CCC2)C[C@@H]1F)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'F', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 15, 1, 1, 1, 11, 8, 12, 6, 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, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 19, 19, 19, 19, 7, 1, 7, 1, 1, 1, 1, 19, 19, 19, 19, 28, 34, 34, 34, 34, 34, 28, 19, 19, 1, 1, 1, 1, 1, 1, 1, 19, 19, 34] 34 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: 80 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074602 none O=C(N[C@@H]1CN(C(=O)C2CCC2)C[C@@H]1F)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'F', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 15, 1, 1, 1, 11, 8, 12, 6, 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, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 19, 19, 19, 1, 1, 1, 1, 6, 14, 14, 14, 14, 14, 6, 1, 1, 19, 19, 19, 19, 19, 19, 19, 1, 1, 14] 34 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 13, 14, 15, 34, 24, 25, 16] set([0, 1, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 35]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.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: REAL250005074602 none O=C(N[C@@H]1CN(C(=O)C2CCC2)C[C@@H]1F)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'F', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 15, 1, 1, 1, 11, 8, 12, 6, 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, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [10, 1, 10, 10, 14, 14, 14, 14, 24, 24, 34, 34, 34, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 10, 14, 14, 34, 34, 34, 34, 34, 34, 34, 14, 14, 1] 34 rigid atoms, others: [1, 35, 17, 18, 19, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 105 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074602 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074602 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074602/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074602 Building REAL250005074603 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074603' /scratch/stefan/7916156/working/building/REAL250005074603 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074603 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074603/0 /scratch/stefan/7916156/working/building/REAL250005074603 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 724) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/724 `/scratch/stefan/7916156/working/3D/724' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1) `REAL250005074603.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074603/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074603 none NC(=O)C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 15, 5, 6, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 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, 24, 29, 14, 24, 14, 14, 7, 14, 7, 1, 7, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 29, 29, 14, 14, 7, 1, 14, 14] 29 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29]) total number of confs: 89 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074603 none NC(=O)C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 15, 5, 6, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 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: [18, 7, 18, 1, 7, 1, 1, 1, 1, 1, 5, 5, 5, 14, 14, 14, 14, 14, 1, 1, 1, 1, 18, 18, 1, 1, 5, 14, 1, 1] 29 rigid atoms, others: [3, 5, 6, 7, 8, 9, 18, 19, 20, 21, 24, 25, 28, 29] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 26, 27]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074603 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074603 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074603/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074603 Building REAL250005074604 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074604' /scratch/stefan/7916156/working/building/REAL250005074604 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074604 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074604/0 /scratch/stefan/7916156/working/building/REAL250005074604 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 725) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/725 `/scratch/stefan/7916156/working/3D/725' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1) `REAL250005074604.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074604/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074604 none CC(C)(C)C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', '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, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 15, 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, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 7, 15, 7, 7, 4, 7, 4, 1, 4, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 7, 7, 5, 1, 7, 7] 15 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: 49 number of broken/clashed sets: 15 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074604 none CC(C)(C)C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', '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, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 15, 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, 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: [4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 5, 7, 1, 1] 15 rigid atoms, others: [32, 33, 4, 37, 6, 7, 8, 9, 10, 19, 20, 21, 22, 36] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35]) total number of confs: 23 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074604 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074604 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074604/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074604 Building REAL250005074605 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074605' /scratch/stefan/7916156/working/building/REAL250005074605 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074605 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074605/0 /scratch/stefan/7916156/working/building/REAL250005074605 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 726) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/726 `/scratch/stefan/7916156/working/3D/726' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C(=O)N2C[C@@H](NC(=O)C3=CC(=O)[N-]O3)[C@@H](F)C2)CC1) `REAL250005074605.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074605.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074605/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074605 none CC1(C(=O)N2C[C@@H](NC(=O)C3=CC(=O)[N-]O3)[C@@H](F)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'F', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 15, 5, 5, 5, 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: [10, 7, 1, 7, 1, 1, 1, 1, 1, 5, 5, 5, 14, 14, 14, 14, 14, 1, 1, 1, 1, 10, 10, 10, 10, 10, 1, 1, 5, 14, 1, 1, 10, 10, 10, 10] 23 rigid atoms, others: [2, 4, 5, 6, 7, 8, 17, 18, 19, 20, 26, 27, 30, 31] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 28, 29, 32, 33, 34, 35]) total number of confs: 50 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074605 none CC1(C(=O)N2C[C@@H](NC(=O)C3=CC(=O)[N-]O3)[C@@H](F)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'F', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 15, 5, 5, 5, 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, 10, 10, 10, 10, 19, 19, 19, 23, 23, 23, 23, 23, 10, 10, 10, 10, 1, 1, 2, 2, 2, 10, 10, 19, 23, 10, 10, 1, 1, 1, 1] 23 rigid atoms, others: [0, 1, 2, 35, 33, 32, 34, 21, 22] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 61 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.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: REAL250005074605 none CC1(C(=O)N2C[C@@H](NC(=O)C3=CC(=O)[N-]O3)[C@@H](F)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'F', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 15, 5, 5, 5, 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, 14, 22, 14, 14, 9, 14, 9, 1, 9, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 23, 23, 23, 23, 23, 14, 14, 9, 1, 14, 14, 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: 63 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074605 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074605 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074605/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074605 Building REAL250005074606 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074606' /scratch/stefan/7916156/working/building/REAL250005074606 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074606 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074606/0 /scratch/stefan/7916156/working/building/REAL250005074606 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 727) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/727 `/scratch/stefan/7916156/working/3D/727' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H]1C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1) `REAL250005074606.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074606/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074606 none C[C@@H]1C[C@H]1C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 15, 5, 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] 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: [24, 24, 24, 24, 6, 24, 1, 6, 1, 1, 1, 1, 1, 6, 6, 6, 16, 16, 16, 16, 16, 1, 1, 1, 1, 24, 24, 24, 24, 24, 1, 1, 6, 16, 1, 1] 41 rigid atoms, others: [34, 35, 6, 8, 9, 10, 11, 12, 21, 22, 23, 24, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 32, 33]) total number of confs: 87 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074606 none C[C@@H]1C[C@H]1C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 15, 5, 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] 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, 1, 1, 8, 8, 24, 24, 24, 24, 38, 38, 38, 41, 41, 41, 41, 41, 24, 24, 24, 24, 2, 2, 2, 1, 1, 24, 24, 38, 41, 24, 24] 41 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35]) 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.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: REAL250005074606 none C[C@@H]1C[C@H]1C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 15, 5, 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] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 41, 41, 30, 41, 16, 30, 16, 16, 7, 16, 7, 1, 7, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 41, 41, 41, 41, 41, 16, 16, 7, 1, 16, 16] 41 rigid atoms, others: [33, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35]) total number of confs: 129 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074606 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074606 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074606/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074606 Building REAL250005074607 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074607' /scratch/stefan/7916156/working/building/REAL250005074607 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074607 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074607/0 /scratch/stefan/7916156/working/building/REAL250005074607 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 728) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/728 `/scratch/stefan/7916156/working/3D/728' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@@H]1C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1) `REAL250005074607.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074607/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074607 none C[C@H]1C[C@@H]1C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 15, 5, 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] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 6, 21, 1, 6, 1, 1, 1, 1, 1, 5, 5, 5, 19, 19, 19, 19, 19, 1, 1, 1, 1, 21, 21, 21, 21, 21, 1, 1, 5, 19, 1, 1] 48 rigid atoms, others: [34, 35, 6, 8, 9, 10, 11, 12, 21, 22, 23, 24, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 32, 33]) total number of confs: 83 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074607 none C[C@H]1C[C@@H]1C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 15, 5, 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] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 8, 8, 21, 21, 21, 21, 42, 42, 42, 48, 48, 48, 48, 48, 21, 21, 21, 21, 2, 2, 2, 1, 1, 21, 21, 42, 48, 21, 21] 48 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35]) 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.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: REAL250005074607 none C[C@H]1C[C@@H]1C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 15, 5, 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] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 48, 38, 48, 19, 38, 19, 19, 9, 19, 9, 1, 9, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 48, 48, 48, 48, 48, 19, 19, 9, 1, 19, 19] 48 rigid atoms, others: [33, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35]) total number of confs: 143 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074607 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074607 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074607/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074607 Building REAL250005074608 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074608' /scratch/stefan/7916156/working/building/REAL250005074608 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074608 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074608/0 /scratch/stefan/7916156/working/building/REAL250005074608 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 729) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/729 `/scratch/stefan/7916156/working/3D/729' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CO)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1) `REAL250005074608.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074608/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074608 none O=C(CO)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 15, 5, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [17, 12, 17, 20, 12, 12, 8, 12, 8, 1, 8, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 20, 20, 60, 12, 12, 8, 1, 12, 12] 60 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29]) total number of confs: 127 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074608 none O=C(CO)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 15, 5, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 8, 1, 1, 1, 1, 1, 5, 5, 5, 12, 12, 12, 12, 12, 1, 1, 1, 1, 8, 8, 24, 1, 1, 5, 12, 1, 1] 60 rigid atoms, others: [1, 4, 5, 6, 7, 8, 17, 18, 19, 20, 24, 25, 28, 29] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 26, 27]) total number of confs: 72 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074608 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074608 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074608/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074608 Building REAL250005074609 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074609' /scratch/stefan/7916156/working/building/REAL250005074609 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074609 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074609/0 /scratch/stefan/7916156/working/building/REAL250005074609 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 730) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/730 `/scratch/stefan/7916156/working/3D/730' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CN(C(=O)C2CCO2)C[C@@H]1F)C1=CC(=O)[N-]O1) `REAL250005074609.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074609/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074609 none O=C(N[C@@H]1CN(C(=O)C2CCO2)C[C@@H]1F)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'F', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 7, 15, 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, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 23, 23, 23, 23, 9, 1, 9, 1, 1, 1, 1, 23, 23, 23, 23, 36, 42, 42, 42, 42, 42, 36, 23, 23, 1, 1, 1, 1, 1, 23, 23, 42] 42 rigid atoms, others: [7, 9, 10, 11, 12, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 31, 32, 33]) total number of confs: 98 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074609 none O=C(N[C@@H]1CN(C(=O)C2CCO2)C[C@@H]1F)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'F', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 7, 15, 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, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 1, 7, 7, 23, 23, 23, 1, 1, 1, 1, 6, 17, 17, 17, 17, 17, 6, 1, 1, 23, 23, 23, 23, 23, 1, 1, 17] 42 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 24, 25, 31] set([0, 1, 33, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30]) 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.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: REAL250005074609 none O=C(N[C@@H]1CN(C(=O)C2CCO2)C[C@@H]1F)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'F', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 7, 15, 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, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 8, 8, 17, 17, 17, 17, 34, 34, 42, 42, 42, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 8, 17, 17, 42, 42, 42, 42, 42, 17, 17, 1] 42 rigid atoms, others: [1, 33, 17, 18, 19, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 125 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074609 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074609 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074609/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074609 Building REAL250005074610 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074610' /scratch/stefan/7916156/working/building/REAL250005074610 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074610 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074610/0 /scratch/stefan/7916156/working/building/REAL250005074610 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 731) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/731 `/scratch/stefan/7916156/working/3D/731' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CN(C(=O)C2COC2)C[C@@H]1F)C1=CC(=O)[N-]O1) `REAL250005074610.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074610/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074610 none O=C(N[C@@H]1CN(C(=O)C2COC2)C[C@@H]1F)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'F', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 15, 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, 7, 7, 3, 7, 3, 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: [21, 21, 14, 14, 14, 14, 7, 1, 7, 1, 1, 1, 1, 14, 14, 14, 14, 21, 24, 24, 24, 24, 24, 21, 14, 14, 1, 1, 1, 1, 1, 14, 14, 24] 24 rigid atoms, others: [7, 9, 10, 11, 12, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 31, 32, 33]) total number of confs: 56 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074610 none O=C(N[C@@H]1CN(C(=O)C2COC2)C[C@@H]1F)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'F', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 15, 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, 7, 7, 3, 7, 3, 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: [6, 6, 1, 1, 1, 1, 1, 1, 5, 5, 14, 14, 14, 1, 1, 1, 1, 6, 12, 12, 12, 12, 12, 6, 1, 1, 14, 14, 14, 14, 14, 1, 1, 12] 24 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 24, 25, 31] set([0, 1, 33, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30]) 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.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: REAL250005074610 none O=C(N[C@@H]1CN(C(=O)C2COC2)C[C@@H]1F)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'F', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 15, 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, 7, 7, 3, 7, 3, 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: [6, 1, 6, 7, 12, 12, 12, 12, 18, 18, 24, 24, 24, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 7, 12, 12, 24, 24, 24, 24, 24, 12, 12, 1] 24 rigid atoms, others: [1, 33, 17, 18, 19, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 77 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074610 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074610 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074610/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074610 Building REAL250005074611 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074611' /scratch/stefan/7916156/working/building/REAL250005074611 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074611 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074611/0 /scratch/stefan/7916156/working/building/REAL250005074611 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 732) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/732 `/scratch/stefan/7916156/working/3D/732' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(C=CCO)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1) `REAL250005074611.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074611/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074611 none O=C(C=CCO)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 5, 12, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 15, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 210 conformations in input total number of sets (complete confs): 210 using faster count positions algorithm for large data unique positions, atoms: [39, 23, 39, 68, 68, 70, 23, 23, 9, 23, 9, 1, 9, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 68, 68, 70, 70, 210, 23, 23, 9, 1, 23, 23] 210 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33]) total number of confs: 421 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074611 none O=C(C=CCO)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 5, 12, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 15, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 210 conformations in input total number of sets (complete confs): 210 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 7, 25, 26, 48, 1, 1, 1, 1, 1, 6, 6, 6, 23, 23, 23, 23, 23, 1, 1, 1, 1, 26, 25, 48, 48, 144, 1, 1, 6, 23, 1, 1] 210 rigid atoms, others: [32, 1, 33, 6, 7, 8, 9, 10, 19, 20, 21, 22, 28, 29] set([0, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 30, 31]) total number of confs: 349 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074611 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074611 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074611/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074611 Building REAL250005074612 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074612' /scratch/stefan/7916156/working/building/REAL250005074612 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074612 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074612/0 /scratch/stefan/7916156/working/building/REAL250005074612 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 733) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/733 `/scratch/stefan/7916156/working/3D/733' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC=CC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1) `REAL250005074612.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074612/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074612 none CCC=CC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [79, 70, 70, 49, 22, 49, 22, 22, 9, 22, 9, 1, 9, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 79, 79, 79, 79, 79, 70, 70, 22, 22, 9, 1, 22, 22] 79 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: 257 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074612 none CCC=CC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [48, 33, 32, 6, 1, 6, 1, 1, 1, 1, 1, 6, 6, 6, 22, 22, 22, 22, 22, 1, 1, 1, 1, 48, 48, 48, 48, 48, 32, 33, 1, 1, 6, 22, 1, 1] 79 rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 10, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 32, 33]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074612 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074612 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074612/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074612 Building REAL250005074613 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074613' /scratch/stefan/7916156/working/building/REAL250005074613 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074613 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074613/0 /scratch/stefan/7916156/working/building/REAL250005074613 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 734) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/734 `/scratch/stefan/7916156/working/3D/734' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1) `REAL250005074613.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074613/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074613 none C#CCCC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 15, 5, 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] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [72, 72, 66, 33, 13, 33, 13, 13, 6, 13, 6, 1, 6, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 72, 72, 72, 66, 66, 13, 13, 6, 1, 13, 13] 72 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33]) total number of confs: 273 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074613 none C#CCCC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 15, 5, 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] 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: [45, 45, 27, 6, 1, 6, 1, 1, 1, 1, 1, 6, 6, 6, 13, 13, 13, 13, 13, 1, 1, 1, 1, 45, 44, 44, 27, 27, 1, 1, 6, 13, 1, 1] 72 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 19, 20, 21, 22, 28, 29] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 30, 31]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074613 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074613 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074613/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074613 Building REAL250005074614 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074614' /scratch/stefan/7916156/working/building/REAL250005074614 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074614 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074614/0 /scratch/stefan/7916156/working/building/REAL250005074614 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 735) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/735 `/scratch/stefan/7916156/working/3D/735' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(O)C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1) `REAL250005074614.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074614/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074614 none C=CC(O)C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 15, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 38, 67, 15, 38, 15, 15, 7, 15, 7, 1, 7, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 67, 67, 67, 67, 201, 15, 15, 7, 1, 15, 15] 201 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33]) total number of confs: 450 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074614 none C=CC(O)C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 15, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [45, 27, 6, 27, 1, 6, 1, 1, 1, 1, 1, 6, 6, 6, 15, 15, 15, 15, 15, 1, 1, 1, 1, 45, 45, 45, 27, 81, 1, 1, 6, 15, 1, 1] 201 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 19, 20, 21, 22, 28, 29] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 30, 31]) total number of confs: 260 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074614 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074614 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074614/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074614 Building REAL250005074615 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074615' /scratch/stefan/7916156/working/building/REAL250005074615 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074615 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074615/0 /scratch/stefan/7916156/working/building/REAL250005074615 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 736) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/736 `/scratch/stefan/7916156/working/3D/736' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1) `REAL250005074615.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074615/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074615 none CC(O)C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 15, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [29, 21, 29, 14, 21, 14, 14, 6, 14, 6, 1, 6, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 29, 29, 29, 29, 87, 14, 14, 6, 1, 14, 14] 87 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: 192 number of broken/clashed sets: 22 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074615 none CC(O)C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 15, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 13, 1, 5, 1, 1, 1, 1, 1, 5, 5, 5, 14, 14, 14, 14, 14, 1, 1, 1, 1, 13, 13, 13, 13, 39, 1, 1, 5, 14, 1, 1] 87 rigid atoms, others: [32, 3, 5, 6, 7, 8, 9, 18, 19, 20, 21, 27, 28, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 29, 30]) total number of confs: 108 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074615 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074615 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074615/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074615 Building REAL250005074616 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074616' /scratch/stefan/7916156/working/building/REAL250005074616 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074616 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074616/0 /scratch/stefan/7916156/working/building/REAL250005074616 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 737) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/737 `/scratch/stefan/7916156/working/3D/737' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1) `REAL250005074616.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074616/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074616 none CC(=O)C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 15, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 23, 27, 12, 23, 12, 12, 7, 12, 7, 1, 7, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 27, 27, 27, 12, 12, 7, 1, 12, 12] 27 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30]) total number of confs: 79 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074616 none CC(=O)C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 15, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 14, 1, 6, 1, 1, 1, 1, 1, 5, 5, 5, 12, 12, 12, 12, 12, 1, 1, 1, 1, 14, 14, 14, 1, 1, 5, 12, 1, 1] 27 rigid atoms, others: [3, 5, 6, 7, 8, 9, 18, 19, 20, 21, 25, 26, 29, 30] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 27, 28]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074616 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074616 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074616/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074616 Building REAL250005074617 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074617' /scratch/stefan/7916156/working/building/REAL250005074617 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074617 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074617/0 /scratch/stefan/7916156/working/building/REAL250005074617 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 738) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/738 `/scratch/stefan/7916156/working/3D/738' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CN(C(=O)C2(O)CC2)C[C@@H]1F)C1=CC(=O)[N-]O1) `REAL250005074617.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074617/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074617 none O=C(N[C@@H]1CN(C(=O)C2(O)CC2)C[C@@H]1F)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'F', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 15, 1, 1, 1, 11, 8, 12, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 14, 14, 14, 14, 8, 1, 8, 1, 1, 1, 1, 14, 14, 14, 14, 26, 30, 30, 30, 30, 30, 26, 14, 14, 6, 1, 1, 1, 1, 14, 14, 30] 90 rigid atoms, others: [7, 9, 10, 11, 12, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33]) total number of confs: 84 number of broken/clashed sets: 15 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074617 none O=C(N[C@@H]1CN(C(=O)C2(O)CC2)C[C@@H]1F)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'F', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 15, 1, 1, 1, 11, 8, 12, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 1, 7, 7, 14, 14, 14, 1, 1, 1, 1, 6, 15, 15, 15, 15, 15, 6, 1, 1, 42, 14, 14, 14, 14, 1, 1, 15] 90 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 24, 25, 31] set([0, 1, 33, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30]) total number of confs: 100 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.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: REAL250005074617 none O=C(N[C@@H]1CN(C(=O)C2(O)CC2)C[C@@H]1F)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'F', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 15, 1, 1, 1, 11, 8, 12, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 15, 15, 15, 15, 22, 22, 30, 30, 30, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 6, 15, 15, 90, 30, 30, 30, 30, 15, 15, 1] 90 rigid atoms, others: [1, 33, 17, 18, 19, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 185 number of broken/clashed sets: 15 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074617 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074617 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074617/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074617 Building REAL250005074618 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074618' /scratch/stefan/7916156/working/building/REAL250005074618 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074618 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074618/0 /scratch/stefan/7916156/working/building/REAL250005074618 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 739) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/739 `/scratch/stefan/7916156/working/3D/739' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CN(C(=O)C2=CCC2)C[C@@H]1F)C1=CC(=O)[N-]O1) `REAL250005074618.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074618/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074618 none O=C(N[C@@H]1CN(C(=O)C2=CCC2)C[C@@H]1F)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'F', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 7, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 20, 20, 20, 20, 9, 1, 9, 1, 1, 1, 1, 20, 20, 20, 20, 29, 32, 32, 32, 32, 32, 29, 20, 20, 1, 1, 1, 1, 1, 20, 20, 32] 32 rigid atoms, others: [7, 9, 10, 11, 12, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 31, 32, 33]) total number of confs: 72 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074618 none O=C(N[C@@H]1CN(C(=O)C2=CCC2)C[C@@H]1F)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'F', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 7, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 1, 1, 1, 1, 1, 1, 6, 6, 20, 20, 20, 1, 1, 1, 1, 5, 19, 19, 19, 19, 19, 5, 1, 1, 20, 20, 20, 20, 20, 1, 1, 19] 32 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 24, 25, 31] set([0, 1, 33, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up 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: REAL250005074618 none O=C(N[C@@H]1CN(C(=O)C2=CCC2)C[C@@H]1F)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'F', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 7, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 9, 9, 19, 19, 19, 19, 32, 32, 32, 32, 32, 19, 19, 19, 19, 1, 1, 1, 1, 1, 1, 9, 19, 19, 32, 32, 32, 32, 32, 19, 19, 1] 32 rigid atoms, others: [1, 33, 17, 18, 19, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 87 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074618 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074618 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074618/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074618 Building REAL250005074619 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074619' /scratch/stefan/7916156/working/building/REAL250005074619 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074619 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074619/0 /scratch/stefan/7916156/working/building/REAL250005074619 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 740) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/740 `/scratch/stefan/7916156/working/3D/740' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1) `REAL250005074619.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074619.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074619/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074619 none CC=CC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 15, 5, 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 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 18, 12, 18, 12, 12, 5, 12, 5, 1, 5, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 22, 22, 22, 22, 22, 12, 12, 5, 1, 12, 12] 22 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32]) total number of confs: 65 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074619 none CC=CC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 15, 5, 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 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [15, 14, 4, 1, 4, 1, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 1, 1, 1, 1, 15, 15, 15, 14, 15, 1, 1, 6, 12, 1, 1] 22 rigid atoms, others: [32, 3, 5, 6, 7, 8, 9, 18, 19, 20, 21, 27, 28, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 29, 30]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074619 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074619 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074619/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074619 Building REAL250005074620 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074620' /scratch/stefan/7916156/working/building/REAL250005074620 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types Protomer extracton resulted in 0 protomers Marking REAL250005074620 as failed and skipping /scratch/stefan/7916156/working /scratch/stefan/7916156 `/scratch/stefan/7916156/working/building/REAL250005074620' -> `/scratch/stefan/7916156/failed/REAL250005074620' Building REAL250005074621 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074621' /scratch/stefan/7916156/working/building/REAL250005074621 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074621 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074621/0 /scratch/stefan/7916156/working/building/REAL250005074621 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 741) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/741 `/scratch/stefan/7916156/working/3D/741' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1) `REAL250005074621.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074621/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074621 none C[C@H](O)C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 15, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [31, 22, 31, 31, 13, 22, 13, 13, 6, 13, 6, 1, 6, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 31, 31, 31, 93, 13, 13, 6, 1, 13, 13] 93 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32]) total number of confs: 204 number of broken/clashed sets: 18 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074621 none C[C@H](O)C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 15, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [17, 6, 17, 17, 1, 6, 1, 1, 1, 1, 1, 6, 6, 6, 13, 13, 13, 13, 13, 1, 1, 1, 1, 17, 17, 17, 51, 1, 1, 6, 13, 1, 1] 93 rigid atoms, others: [32, 4, 6, 7, 8, 9, 10, 19, 20, 21, 22, 27, 28, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 29, 30]) total number of confs: 132 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074621 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074621 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074621/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074621 Building REAL250005074622 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074622' /scratch/stefan/7916156/working/building/REAL250005074622 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074622 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074622/0 /scratch/stefan/7916156/working/building/REAL250005074622 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 742) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/742 `/scratch/stefan/7916156/working/3D/742' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H]1C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1) `REAL250005074622.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074622/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074622 none C[C@@H]1C[C@H]1C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 15, 5, 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] 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: [24, 24, 24, 24, 6, 24, 1, 6, 1, 1, 1, 1, 1, 6, 6, 6, 16, 16, 16, 16, 16, 1, 1, 1, 1, 24, 24, 24, 24, 24, 1, 1, 6, 16, 1, 1] 41 rigid atoms, others: [34, 35, 6, 8, 9, 10, 11, 12, 21, 22, 23, 24, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 32, 33]) total number of confs: 87 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074622 none C[C@@H]1C[C@H]1C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 15, 5, 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] 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, 1, 1, 8, 8, 24, 24, 24, 24, 38, 38, 38, 41, 41, 41, 41, 41, 24, 24, 24, 24, 2, 2, 2, 1, 1, 24, 24, 38, 41, 24, 24] 41 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35]) 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.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: REAL250005074622 none C[C@@H]1C[C@H]1C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 15, 5, 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] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 41, 41, 30, 41, 16, 30, 16, 16, 7, 16, 7, 1, 7, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 41, 41, 41, 41, 41, 16, 16, 7, 1, 16, 16] 41 rigid atoms, others: [33, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35]) total number of confs: 129 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074622 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074622 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074622/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074622 Building REAL250005074623 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074623' /scratch/stefan/7916156/working/building/REAL250005074623 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074623 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074623/0 /scratch/stefan/7916156/working/building/REAL250005074623 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 743) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/743 `/scratch/stefan/7916156/working/3D/743' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)CC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1) `REAL250005074623.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074623/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074623 none C=C(C)CC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 67, 34, 13, 34, 13, 13, 7, 13, 7, 1, 7, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 67, 67, 67, 67, 67, 67, 67, 13, 13, 7, 1, 13, 13] 67 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: 245 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074623 none C=C(C)CC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [49, 36, 49, 7, 1, 7, 1, 1, 1, 1, 1, 5, 5, 5, 13, 13, 13, 13, 13, 1, 1, 1, 1, 49, 49, 49, 49, 49, 36, 36, 1, 1, 5, 13, 1, 1] 67 rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 10, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 32, 33]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074623 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074623 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074623/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074623 Building REAL250005074624 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074624' /scratch/stefan/7916156/working/building/REAL250005074624 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074624 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074624/0 /scratch/stefan/7916156/working/building/REAL250005074624 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 744) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/744 `/scratch/stefan/7916156/working/3D/744' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1) `REAL250005074624.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074624/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074624 none C=CCC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 15, 5, 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 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [66, 66, 41, 18, 41, 18, 18, 8, 18, 8, 1, 8, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 66, 66, 66, 66, 66, 18, 18, 8, 1, 18, 18] 66 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32]) total number of confs: 239 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074624 none C=CCC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 15, 5, 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 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [48, 27, 6, 1, 6, 1, 1, 1, 1, 1, 6, 6, 6, 18, 18, 18, 18, 18, 1, 1, 1, 1, 48, 48, 48, 27, 27, 1, 1, 6, 18, 1, 1] 66 rigid atoms, others: [32, 3, 5, 6, 7, 8, 9, 18, 19, 20, 21, 27, 28, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 29, 30]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074624 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074624 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074624/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074624 Building REAL250005074625 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074625' /scratch/stefan/7916156/working/building/REAL250005074625 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074625 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074625/0 /scratch/stefan/7916156/working/building/REAL250005074625 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 745) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/745 `/scratch/stefan/7916156/working/3D/745' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1) `REAL250005074625.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074625/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074625 none N#CCC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 15, 5, 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] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 26, 18, 26, 18, 18, 11, 18, 11, 1, 11, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 38, 38, 18, 18, 11, 1, 18, 18] 38 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29]) total number of confs: 139 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074625 none N#CCC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 15, 5, 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] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 6, 1, 6, 1, 1, 1, 1, 1, 5, 5, 5, 18, 18, 18, 18, 18, 1, 1, 1, 1, 18, 18, 1, 1, 5, 18, 1, 1] 38 rigid atoms, others: [3, 5, 6, 7, 8, 9, 18, 19, 20, 21, 24, 25, 28, 29] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 26, 27]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074625 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074625 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074625/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074625 Building REAL250005074626 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074626' /scratch/stefan/7916156/working/building/REAL250005074626 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074626 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074626/0 /scratch/stefan/7916156/working/building/REAL250005074626 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 746) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/746 `/scratch/stefan/7916156/working/3D/746' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCF)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1) `REAL250005074626.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074626/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074626 none O=C(CCF)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 15, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 15, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [27, 16, 27, 56, 56, 16, 16, 7, 16, 7, 1, 7, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 56, 56, 56, 56, 16, 16, 8, 1, 16, 16] 56 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]) total number of confs: 207 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074626 none O=C(CCF)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 15, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 15, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 17, 29, 1, 1, 1, 1, 1, 6, 6, 6, 16, 16, 16, 16, 16, 1, 1, 1, 1, 17, 17, 29, 29, 1, 1, 6, 16, 1, 1] 56 rigid atoms, others: [1, 5, 6, 7, 8, 9, 18, 19, 20, 21, 26, 27, 30, 31] set([0, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 28, 29]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074626 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074626 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074626/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074626 Building REAL250005074627 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074627' /scratch/stefan/7916156/working/building/REAL250005074627 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074627 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074627/0 /scratch/stefan/7916156/working/building/REAL250005074627 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 747) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/747 `/scratch/stefan/7916156/working/3D/747' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1) `REAL250005074627.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074627.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074627/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074627 none C[C@@H](O)C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 15, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [29, 21, 29, 29, 14, 21, 14, 14, 6, 14, 6, 1, 6, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 29, 29, 29, 87, 14, 14, 6, 1, 14, 14] 87 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32]) total number of confs: 192 number of broken/clashed sets: 19 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074627 none C[C@@H](O)C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 15, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 13, 13, 1, 5, 1, 1, 1, 1, 1, 5, 5, 5, 14, 14, 14, 14, 14, 1, 1, 1, 1, 13, 13, 13, 39, 1, 1, 5, 14, 1, 1] 87 rigid atoms, others: [32, 4, 6, 7, 8, 9, 10, 19, 20, 21, 22, 27, 28, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 29, 30]) total number of confs: 108 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074627 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074627 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074627/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074627 Building REAL250005074628 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074628' /scratch/stefan/7916156/working/building/REAL250005074628 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074628 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074628/0 /scratch/stefan/7916156/working/building/REAL250005074628 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 748) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/748 `/scratch/stefan/7916156/working/3D/748' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C1CC1C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1) `REAL250005074628.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074628.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074628/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074628 none C=C1CC1C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 15, 5, 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] 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: [17, 17, 17, 4, 1, 4, 1, 1, 1, 1, 1, 5, 5, 5, 13, 13, 13, 13, 13, 1, 1, 1, 1, 17, 17, 17, 17, 17, 1, 1, 5, 13, 1, 1] 34 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 19, 20, 21, 22, 28, 29] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 30, 31]) total number of confs: 64 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074628 none C=C1CC1C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 15, 5, 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] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 8, 8, 17, 17, 17, 17, 29, 29, 29, 34, 34, 34, 34, 34, 17, 17, 17, 17, 1, 1, 1, 1, 1, 17, 17, 29, 34, 17, 17] 34 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 25, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074628 none C=C1CC1C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 15, 5, 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] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 20, 13, 20, 13, 13, 8, 13, 8, 1, 8, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 34, 34, 34, 34, 34, 13, 13, 8, 1, 13, 13] 34 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33]) total number of confs: 107 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074628 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074628 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074628/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074628 Building REAL250005074629 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074629' /scratch/stefan/7916156/working/building/REAL250005074629 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074629 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074629/0 /scratch/stefan/7916156/working/building/REAL250005074629 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 749) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/749 `/scratch/stefan/7916156/working/3D/749' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC1C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1) `REAL250005074629.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074629/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074629 none CC1=CC1C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 15, 5, 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] 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: [22, 22, 22, 7, 1, 7, 1, 1, 1, 1, 1, 5, 5, 5, 18, 18, 18, 18, 18, 1, 1, 1, 1, 22, 22, 22, 22, 22, 1, 1, 5, 18, 1, 1] 45 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 19, 20, 21, 22, 28, 29] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 30, 31]) total number of confs: 82 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074629 none CC1=CC1C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 15, 5, 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] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 9, 9, 22, 22, 22, 22, 40, 40, 40, 45, 45, 45, 45, 45, 22, 22, 22, 22, 2, 2, 2, 1, 1, 22, 22, 40, 45, 22, 22] 45 rigid atoms, others: [0, 1, 2, 3, 4, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074629 none CC1=CC1C(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 15, 5, 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] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 45, 29, 18, 29, 18, 18, 10, 18, 10, 1, 10, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 45, 45, 45, 45, 45, 18, 18, 10, 1, 18, 18] 45 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33]) total number of confs: 135 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074629 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074629 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074629/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074629 Building REAL250005074630 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074630' /scratch/stefan/7916156/working/building/REAL250005074630 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074630 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074630/0 /scratch/stefan/7916156/working/building/REAL250005074630 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 750) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/750 `/scratch/stefan/7916156/working/3D/750' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1) `REAL250005074630.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074630/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074630 none C=CC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 15, 5, 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] 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, 12, 19, 12, 12, 6, 12, 5, 1, 5, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 19, 19, 19, 12, 12, 6, 1, 12, 12] 19 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29]) total number of confs: 55 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074630 none C=CC(=O)N1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 15, 5, 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] 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: [12, 6, 1, 6, 1, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 1, 1, 1, 1, 12, 13, 13, 1, 1, 6, 12, 1, 1] 19 rigid atoms, others: [2, 4, 5, 6, 7, 8, 17, 18, 19, 20, 24, 25, 28, 29] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 26, 27]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074630 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074630 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074630/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074630 Building REAL250005074631 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074631' /scratch/stefan/7916156/working/building/REAL250005074631 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074631 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074631/0 /scratch/stefan/7916156/working/building/REAL250005074631 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 751) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/751 `/scratch/stefan/7916156/working/3D/751' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC1CC2OCCC2N1C(=O)C1=CC(=O)[N-]O1) `REAL250005074631.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074631/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074631 none CC(=O)NCC1CC2OCCC2N1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', '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, 1, 11, 8, 5, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 31, 17, 17, 17, 17, 17, 17, 17, 17, 9, 1, 9, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 31, 31, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1] 33 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: 104 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074631 none CC(=O)NCC1CC2OCCC2N1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', '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, 1, 11, 8, 5, 5, 5, 5, 12, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 17, 17, 17, 17, 17, 16, 16, 16, 16, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17] 33 rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 36, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074631 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074631 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074631/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074631 Building REAL250005074632 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074632' /scratch/stefan/7916156/working/building/REAL250005074632 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074632 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074632/0 /scratch/stefan/7916156/working/building/REAL250005074632 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 752) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/752 `/scratch/stefan/7916156/working/3D/752' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1C(CNC(=O)C2=CC(=O)[N-]O2)CC2OCCC21) `REAL250005074632.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074632/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074632 none CC(=O)N1C(CNC(=O)C2=CC(=O)[N-]O2)CC2OCCC21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 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, 20, 27, 20, 16, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20, 27, 27, 27, 20, 16, 16, 6, 1, 20, 20, 20, 20, 20, 20, 20, 20] 27 rigid atoms, others: [7, 9, 10, 11, 12, 13, 14, 28] set([0, 1, 2, 3, 4, 5, 6, 8, 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: 96 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074632 none CC(=O)N1C(CNC(=O)C2=CC(=O)[N-]O2)CC2OCCC21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 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: [5, 1, 5, 1, 1, 1, 8, 16, 16, 16, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 16, 20, 1, 1, 1, 1, 1, 1, 1, 1] 27 rigid atoms, others: [32, 1, 34, 3, 4, 5, 35, 33, 15, 16, 17, 18, 19, 20, 24, 36, 29, 30, 31] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 25, 26, 27, 28]) total number of confs: 67 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074632 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074632 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074632/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074632 Building REAL250005074633 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074633' /scratch/stefan/7916156/working/building/REAL250005074633 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074633 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074633/0 /scratch/stefan/7916156/working/building/REAL250005074633 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 753) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/753 `/scratch/stefan/7916156/working/3D/753' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005074633.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074633/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074633 none CCC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [58, 45, 45, 45, 29, 29, 29, 29, 9, 1, 9, 1, 1, 1, 1, 1, 1, 29, 30, 30, 30, 58, 58, 58, 58, 58, 45, 29, 29, 1, 29, 30, 30, 30, 30] 58 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34]) total number of confs: 188 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074633 none CCC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [28, 5, 5, 5, 1, 1, 1, 1, 1, 1, 6, 6, 29, 30, 30, 30, 29, 1, 1, 1, 1, 28, 28, 28, 28, 28, 5, 1, 1, 29, 1, 1, 2, 2, 2] 58 rigid atoms, others: [4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 27, 28, 30, 31] set([0, 1, 2, 3, 33, 32, 10, 11, 12, 13, 14, 15, 16, 34, 21, 22, 23, 24, 25, 26, 29]) total number of confs: 142 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074633 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074633 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074633/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074633 Building REAL250005074634 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074634' /scratch/stefan/7916156/working/building/REAL250005074634 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074634 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074634/0 /scratch/stefan/7916156/working/building/REAL250005074634 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 754) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/754 `/scratch/stefan/7916156/working/3D/754' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005074634.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074634/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074634 none COCCC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 184 conformations in input total number of sets (complete confs): 184 using faster count positions algorithm for large data unique positions, atoms: [184, 183, 164, 68, 68, 68, 30, 30, 30, 30, 9, 1, 9, 1, 1, 1, 1, 1, 1, 29, 29, 30, 29, 184, 184, 184, 183, 183, 164, 164, 68, 30, 30, 1, 30, 30, 30, 30, 30] 184 rigid atoms, others: [33, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38]) total number of confs: 719 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074634 none COCCC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 184 conformations in input total number of sets (complete confs): 184 using faster count positions algorithm for large data unique positions, atoms: [101, 62, 32, 5, 5, 5, 1, 1, 1, 1, 1, 1, 6, 6, 29, 30, 30, 30, 30, 1, 1, 1, 1, 101, 101, 101, 62, 62, 32, 32, 5, 1, 1, 29, 1, 1, 2, 2, 2] 184 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 33, 36, 37, 38]) total number of confs: 379 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074634 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074634 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074634/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074634 Building REAL250005074635 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074635' /scratch/stefan/7916156/working/building/REAL250005074635 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074635 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074635/0 /scratch/stefan/7916156/working/building/REAL250005074635 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 755) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/755 `/scratch/stefan/7916156/working/3D/755' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005074635.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074635/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074635 none CC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 15, 15, 15, 15, 8, 1, 8, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 18, 18, 18, 18, 15, 15, 1, 15, 15, 15, 15, 15] 18 rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31]) total number of confs: 41 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074635 none CC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 1, 1, 6, 6, 15, 15, 15, 15, 15, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 15, 1, 1, 2, 2, 2] 18 rigid atoms, others: [3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 24, 25, 27, 28] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 26, 29, 30, 31]) total number of confs: 41 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074635 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074635 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074635/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074635 Building REAL250005074636 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074636' /scratch/stefan/7916156/working/building/REAL250005074636 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074636 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074636/0 /scratch/stefan/7916156/working/building/REAL250005074636 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 756) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/756 `/scratch/stefan/7916156/working/3D/756' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C1CC1) `REAL250005074636.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074636/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074636 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 28, 10, 1, 10, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 36, 36, 36, 65, 65, 28, 28, 28, 28, 28, 1, 28, 28, 36, 65, 65, 65, 65, 65] 65 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 27] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 167 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074636 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 28, 28, 28, 28, 28, 1, 1, 1, 1, 5, 5, 5, 32, 32, 2, 2, 2, 1, 1, 28, 1, 1, 5, 32, 32, 32, 32, 32] 65 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 25, 26, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 27, 30, 31, 32, 33, 34, 35]) total number of confs: 120 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.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: REAL250005074636 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 32, 32, 32, 32, 58, 58, 65, 65, 65, 65, 65, 32, 12, 32, 12, 1, 12, 1, 1, 1, 32, 32, 32, 32, 32, 65, 32, 32, 12, 1, 1, 1, 1, 1] 65 rigid atoms, others: [32, 33, 34, 35, 17, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 184 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074636 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074636 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074636/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074636 Building REAL250005074637 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074637' /scratch/stefan/7916156/working/building/REAL250005074637 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074637 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074637/0 /scratch/stefan/7916156/working/building/REAL250005074637 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 757) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/757 `/scratch/stefan/7916156/working/3D/757' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C1CCC1) `REAL250005074637.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074637/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074637 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 26, 9, 1, 9, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 42, 42, 42, 78, 78, 78, 27, 27, 27, 26, 26, 1, 27, 27, 42, 78, 78, 78, 78, 78, 78, 78] 78 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 214 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074637 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 26, 26, 26, 26, 26, 1, 1, 1, 1, 5, 5, 5, 29, 29, 29, 2, 2, 2, 1, 1, 27, 1, 1, 5, 29, 29, 29, 29, 29, 29, 29] 78 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 26, 27, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 113 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.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: REAL250005074637 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 29, 29, 29, 69, 69, 78, 78, 78, 78, 78, 29, 10, 29, 10, 1, 10, 1, 1, 1, 1, 29, 29, 29, 29, 29, 78, 29, 29, 10, 1, 1, 1, 1, 1, 1, 1] 78 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 17, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 209 number of broken/clashed sets: 5 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074637 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074637 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074637/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074637 Building REAL250005074638 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074638' /scratch/stefan/7916156/working/building/REAL250005074638 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074638 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074638/0 /scratch/stefan/7916156/working/building/REAL250005074638 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 758) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/758 `/scratch/stefan/7916156/working/3D/758' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)CC1CC1) `REAL250005074638.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074638/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074638 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)CC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 138 conformations in input total number of sets (complete confs): 138 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 33, 33, 10, 1, 10, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 61, 61, 61, 119, 138, 138, 33, 33, 33, 33, 33, 1, 33, 33, 61, 119, 119, 138, 138, 138, 138, 138] 138 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 506 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074638 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)CC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 138 conformations in input total number of sets (complete confs): 138 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 33, 33, 33, 33, 33, 1, 1, 1, 1, 5, 5, 5, 39, 57, 57, 2, 2, 2, 1, 1, 33, 1, 1, 5, 39, 39, 57, 57, 57, 57, 57] 138 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 26, 27, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 248 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.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: REAL250005074638 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)CC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 138 conformations in input total number of sets (complete confs): 138 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 57, 57, 57, 57, 112, 112, 138, 138, 138, 138, 138, 57, 22, 57, 22, 3, 22, 1, 1, 1, 1, 57, 57, 57, 57, 57, 138, 57, 57, 22, 3, 3, 1, 1, 1, 1, 1] 138 rigid atoms, others: [34, 35, 36, 37, 38, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 381 number of broken/clashed sets: 8 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074638 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074638 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074638/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074638 Building REAL250005074639 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074639' /scratch/stefan/7916156/working/building/REAL250005074639 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074639 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074639/0 /scratch/stefan/7916156/working/building/REAL250005074639 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 759) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/759 `/scratch/stefan/7916156/working/3D/759' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C(C)(C)F) `REAL250005074639.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074639.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074639/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074639 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C(C)(C)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 24, 23, 9, 1, 9, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 43, 43, 43, 70, 70, 70, 24, 24, 24, 23, 23, 1, 24, 24, 43, 70, 70, 70, 70, 70, 70] 70 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 237 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074639 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C(C)(C)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 23, 23, 23, 23, 23, 1, 1, 1, 1, 5, 5, 5, 26, 26, 26, 2, 2, 2, 1, 1, 24, 1, 1, 5, 26, 26, 26, 26, 26, 26] 70 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 26, 27, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 126 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074639 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074639 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074639/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074639 Building REAL250005074640 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074640' /scratch/stefan/7916156/working/building/REAL250005074640 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074640 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074640/0 /scratch/stefan/7916156/working/building/REAL250005074640 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 760) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/760 `/scratch/stefan/7916156/working/3D/760' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005074640.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074640/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074640 none COCC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [88, 88, 53, 53, 53, 26, 26, 26, 26, 9, 1, 9, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 88, 88, 88, 88, 88, 53, 26, 26, 1, 26, 26, 26, 26, 26] 88 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 304 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074640 none COCC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [46, 33, 5, 5, 5, 1, 1, 1, 1, 1, 1, 6, 6, 26, 26, 26, 26, 26, 1, 1, 1, 1, 46, 46, 46, 33, 33, 5, 1, 1, 26, 1, 1, 2, 2, 2] 88 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 28, 29, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 30, 33, 34, 35]) total number of confs: 174 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074640 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074640 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074640/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074640 Building REAL250005074641 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074641' /scratch/stefan/7916156/working/building/REAL250005074641 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074641 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074641/0 /scratch/stefan/7916156/working/building/REAL250005074641 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 761) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/761 `/scratch/stefan/7916156/working/3D/761' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005074641.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074641.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074641/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074641 none CCCC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [109, 108, 63, 63, 63, 33, 33, 33, 33, 9, 1, 9, 1, 1, 1, 1, 1, 1, 32, 32, 33, 33, 109, 109, 109, 109, 109, 108, 108, 63, 33, 33, 1, 33, 33, 33, 33, 33] 109 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37]) total number of confs: 384 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074641 none CCCC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [38, 29, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 33, 33, 33, 33, 33, 1, 1, 1, 1, 44, 44, 44, 44, 44, 29, 29, 5, 1, 1, 32, 1, 1, 2, 2, 2] 109 rigid atoms, others: [33, 34, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 32, 35, 36, 37]) total number of confs: 272 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074641 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074641 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074641/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074641 Building REAL250005074642 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074642' /scratch/stefan/7916156/working/building/REAL250005074642 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074642 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074642/0 /scratch/stefan/7916156/working/building/REAL250005074642 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 762) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/762 `/scratch/stefan/7916156/working/3D/762' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005074642.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074642/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074642 none CC(C)CC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [62, 64, 64, 40, 40, 40, 24, 24, 24, 24, 8, 1, 8, 1, 1, 1, 1, 1, 1, 23, 23, 24, 24, 64, 64, 64, 64, 64, 64, 64, 64, 64, 40, 24, 24, 1, 24, 24, 24, 24, 24] 64 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: 248 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074642 none CC(C)CC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [15, 16, 18, 5, 5, 5, 1, 1, 1, 1, 1, 1, 6, 7, 23, 24, 24, 24, 24, 1, 1, 1, 1, 18, 18, 18, 18, 18, 18, 18, 16, 16, 5, 1, 1, 23, 1, 1, 2, 2, 2] 64 rigid atoms, others: [33, 34, 36, 37, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 38, 39, 40]) total number of confs: 128 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074642 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074642 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074642/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074642 Building REAL250005074643 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074643' /scratch/stefan/7916156/working/building/REAL250005074643 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074643 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074643/0 /scratch/stefan/7916156/working/building/REAL250005074643 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 763) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/763 `/scratch/stefan/7916156/working/3D/763' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC1C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005074643.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074643/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074643 none CC1CC1C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 20, 5, 5, 5, 1, 1, 1, 1, 1, 1, 6, 6, 22, 22, 22, 22, 22, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 5, 1, 1, 22, 1, 1, 2, 2, 2] 67 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 33, 36, 37, 38]) total number of confs: 89 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074643 none CC1CC1C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 9, 9, 9, 20, 20, 20, 20, 49, 49, 67, 67, 67, 67, 67, 20, 20, 20, 20, 2, 2, 2, 1, 1, 1, 1, 9, 20, 20, 67, 20, 20, 20, 20, 20] 67 rigid atoms, others: [0, 1, 2, 3, 4, 26, 27, 28, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 179 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.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: REAL250005074643 none CC1CC1C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 67, 44, 44, 44, 22, 22, 22, 22, 10, 1, 10, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 67, 67, 67, 67, 67, 67, 67, 44, 22, 22, 1, 22, 22, 22, 22, 22] 67 rigid atoms, others: [33, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38]) total number of confs: 202 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074643 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074643 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074643/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074643 Building REAL250005074644 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074644' /scratch/stefan/7916156/working/building/REAL250005074644 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074644 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074644/0 /scratch/stefan/7916156/working/building/REAL250005074644 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 764) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/764 `/scratch/stefan/7916156/working/3D/764' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005074644.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074644/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074644 none CCOCC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 148 conformations in input total number of sets (complete confs): 148 using faster count positions algorithm for large data unique positions, atoms: [148, 148, 137, 64, 64, 64, 27, 27, 27, 26, 9, 1, 9, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 148, 148, 148, 148, 148, 137, 137, 64, 26, 26, 1, 27, 27, 27, 27, 27] 148 rigid atoms, others: [33, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38]) total number of confs: 510 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074644 none CCOCC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 148 conformations in input total number of sets (complete confs): 148 using faster count positions algorithm for large data unique positions, atoms: [91, 84, 38, 5, 5, 5, 1, 1, 1, 1, 1, 1, 6, 6, 27, 27, 27, 26, 26, 1, 1, 1, 1, 91, 91, 91, 91, 91, 38, 38, 5, 1, 1, 27, 1, 1, 2, 2, 2] 148 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 33, 36, 37, 38]) total number of confs: 281 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074644 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074644 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074644/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074644 Building REAL250005074645 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074645' /scratch/stefan/7916156/working/building/REAL250005074645 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074645 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074645/0 /scratch/stefan/7916156/working/building/REAL250005074645 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 765) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/765 `/scratch/stefan/7916156/working/3D/765' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)=CC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005074645.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074645/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074645 none CC(C)=CC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 48, 48, 48, 27, 27, 27, 27, 9, 1, 9, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 63, 63, 63, 63, 63, 63, 63, 48, 27, 27, 1, 27, 27, 27, 27, 27] 63 rigid atoms, others: [33, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38]) total number of confs: 174 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074645 none CC(C)=CC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 15, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 27, 27, 27, 27, 27, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 5, 1, 1, 27, 1, 1, 2, 2, 2] 63 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 33, 36, 37, 38]) total number of confs: 85 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074645 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074645 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074645/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074645 Building REAL250005074646 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074646' /scratch/stefan/7916156/working/building/REAL250005074646 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074646 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074646/0 /scratch/stefan/7916156/working/building/REAL250005074646 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 766) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/766 `/scratch/stefan/7916156/working/3D/766' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSCC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005074646.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074646/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074646 none CSCC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [151, 138, 64, 64, 64, 29, 29, 29, 29, 10, 1, 10, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 151, 151, 151, 138, 138, 64, 29, 29, 1, 29, 29, 29, 29, 29] 151 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 516 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074646 none CSCC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [83, 35, 5, 5, 5, 1, 1, 1, 1, 1, 1, 6, 6, 29, 29, 29, 29, 29, 1, 1, 1, 1, 81, 83, 83, 35, 35, 5, 1, 1, 29, 1, 1, 2, 2, 2] 151 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 28, 29, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 30, 33, 34, 35]) total number of confs: 235 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074646 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074646 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074646/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074646 Building REAL250005074647 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074647' /scratch/stefan/7916156/working/building/REAL250005074647 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074647 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074647/0 /scratch/stefan/7916156/working/building/REAL250005074647 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 767) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/767 `/scratch/stefan/7916156/working/3D/767' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005074647.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074647.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074647/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074647 none CCCCC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 198 conformations in input total number of sets (complete confs): 198 using faster count positions algorithm for large data unique positions, atoms: [196, 193, 172, 69, 69, 69, 30, 30, 30, 30, 9, 1, 9, 1, 1, 1, 1, 1, 1, 29, 29, 30, 30, 196, 198, 198, 198, 198, 194, 194, 172, 172, 69, 30, 30, 1, 30, 30, 30, 30, 30] 198 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: 816 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074647 none CCCCC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 198 conformations in input total number of sets (complete confs): 198 using faster count positions algorithm for large data unique positions, atoms: [88, 48, 33, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 30, 30, 30, 30, 30, 1, 1, 1, 1, 88, 94, 94, 88, 91, 57, 57, 33, 33, 5, 1, 1, 29, 1, 1, 2, 2, 2] 198 rigid atoms, others: [33, 34, 36, 37, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 38, 39, 40]) total number of confs: 518 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074647 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074647 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074647/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074647 Building REAL250005074648 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074648' /scratch/stefan/7916156/working/building/REAL250005074648 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074648 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074648/0 /scratch/stefan/7916156/working/building/REAL250005074648 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 768) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/768 `/scratch/stefan/7916156/working/3D/768' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005074648.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074648/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074648 none CC(C)C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [68, 52, 68, 52, 52, 35, 35, 35, 35, 9, 1, 9, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 68, 68, 68, 68, 68, 68, 68, 52, 35, 35, 1, 35, 35, 35, 35, 35] 68 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37]) total number of confs: 207 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074648 none CC(C)C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [24, 5, 24, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 35, 35, 35, 35, 35, 1, 1, 1, 1, 24, 24, 24, 24, 24, 24, 24, 5, 1, 1, 35, 1, 1, 2, 2, 2] 68 rigid atoms, others: [33, 34, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 32, 35, 36, 37]) total number of confs: 134 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074648 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074648 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074648/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074648 Building REAL250005074649 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074649' /scratch/stefan/7916156/working/building/REAL250005074649 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074649 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074649/0 /scratch/stefan/7916156/working/building/REAL250005074649 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 769) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/769 `/scratch/stefan/7916156/working/3D/769' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005074649.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074649.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074649/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074649 none CCC(C)C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 106 conformations in input total number of sets (complete confs): 106 using faster count positions algorithm for large data unique positions, atoms: [106, 105, 59, 105, 59, 59, 30, 30, 30, 30, 10, 1, 10, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 106, 106, 106, 106, 106, 105, 105, 105, 105, 59, 30, 30, 1, 30, 30, 30, 30, 30] 106 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: 363 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074649 none CCC(C)C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 106 conformations in input total number of sets (complete confs): 106 using faster count positions algorithm for large data unique positions, atoms: [38, 30, 5, 30, 5, 5, 1, 1, 1, 1, 1, 1, 6, 6, 30, 30, 30, 30, 30, 1, 1, 1, 1, 42, 42, 42, 42, 42, 30, 30, 30, 30, 5, 1, 1, 30, 1, 1, 2, 2, 2] 106 rigid atoms, others: [33, 34, 36, 37, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 38, 39, 40]) total number of confs: 241 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074649 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074649 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074649/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074649 Building REAL250005074650 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074650' /scratch/stefan/7916156/working/building/REAL250005074650 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074650 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074650/0 /scratch/stefan/7916156/working/building/REAL250005074650 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 770) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/770 `/scratch/stefan/7916156/working/3D/770' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005074650.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074650/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074650 none COC(C)C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [61, 61, 42, 61, 42, 42, 25, 25, 25, 25, 9, 1, 9, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 61, 61, 61, 61, 61, 61, 61, 42, 25, 25, 1, 25, 25, 25, 25, 25] 61 rigid atoms, others: [33, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38]) total number of confs: 200 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074650 none COC(C)C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [28, 21, 5, 21, 5, 5, 1, 1, 1, 1, 1, 1, 6, 6, 25, 25, 25, 25, 25, 1, 1, 1, 1, 28, 28, 28, 21, 21, 21, 21, 5, 1, 1, 25, 1, 1, 2, 2, 2] 61 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 33, 36, 37, 38]) total number of confs: 125 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074650 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074650 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074650/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074650 Building REAL250005074651 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074651' /scratch/stefan/7916156/working/building/REAL250005074651 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074651 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074651/0 /scratch/stefan/7916156/working/building/REAL250005074651 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 771) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/771 `/scratch/stefan/7916156/working/3D/771' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005074651.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074651.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074651/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074651 none C=CCCC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 173, 65, 65, 65, 27, 27, 27, 27, 9, 1, 9, 1, 1, 1, 1, 1, 1, 26, 26, 27, 26, 201, 201, 201, 201, 201, 173, 173, 65, 27, 27, 1, 27, 27, 27, 27, 27] 201 rigid atoms, others: [33, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38]) total number of confs: 796 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074651 none C=CCCC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [119, 64, 35, 5, 5, 5, 1, 1, 1, 1, 1, 1, 6, 6, 26, 27, 27, 27, 27, 1, 1, 1, 1, 119, 119, 119, 64, 64, 35, 35, 5, 1, 1, 26, 1, 1, 2, 2, 2] 201 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 33, 36, 37, 38]) total number of confs: 498 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074651 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074651 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074651/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074651 Building REAL250005074652 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074652' /scratch/stefan/7916156/working/building/REAL250005074652 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074652 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074652/0 /scratch/stefan/7916156/working/building/REAL250005074652 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 772) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/772 `/scratch/stefan/7916156/working/3D/772' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=C(C)C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005074652.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074652/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074652 none CC=C(C)C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [64, 64, 37, 64, 37, 37, 26, 26, 26, 26, 9, 1, 9, 1, 1, 1, 1, 1, 1, 25, 25, 26, 26, 64, 64, 64, 64, 64, 64, 64, 37, 26, 26, 1, 26, 26, 26, 26, 26] 64 rigid atoms, others: [33, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38]) total number of confs: 178 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074652 none CC=C(C)C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 5, 27, 5, 5, 1, 1, 1, 1, 1, 1, 6, 6, 25, 26, 26, 26, 26, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 27, 5, 1, 1, 25, 1, 1, 2, 2, 2] 64 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 33, 36, 37, 38]) total number of confs: 108 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074652 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074652 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074652/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074652 Building REAL250005074653 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074653' /scratch/stefan/7916156/working/building/REAL250005074653 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074653 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074653/0 /scratch/stefan/7916156/working/building/REAL250005074653 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 773) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/773 `/scratch/stefan/7916156/working/3D/773' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C1(C)CC1) `REAL250005074653.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074653/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074653 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C1(C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 19, 9, 1, 9, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 25, 25, 25, 82, 82, 82, 19, 19, 19, 19, 19, 1, 19, 19, 25, 82, 82, 82, 82, 82, 82, 82] 82 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 215 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074653 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C1(C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 19, 19, 19, 19, 19, 1, 1, 1, 1, 4, 4, 4, 19, 19, 19, 2, 2, 2, 1, 1, 19, 1, 1, 4, 19, 19, 19, 19, 19, 19, 19] 82 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 26, 27, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 81 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.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: REAL250005074653 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C1(C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 19, 19, 19, 68, 68, 82, 82, 82, 82, 82, 19, 6, 19, 6, 1, 6, 1, 1, 1, 1, 19, 19, 19, 19, 19, 82, 19, 19, 6, 2, 2, 2, 1, 1, 1, 1] 82 rigid atoms, others: [35, 36, 37, 38, 17, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 213 number of broken/clashed sets: 7 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074653 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074653 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074653/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074653 Building REAL250005074654 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074654' /scratch/stefan/7916156/working/building/REAL250005074654 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074654 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074654/0 /scratch/stefan/7916156/working/building/REAL250005074654 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 774) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/774 `/scratch/stefan/7916156/working/3D/774' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H]1C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005074654.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074654/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074654 none C[C@@H]1C[C@H]1C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 32, 32, 5, 32, 5, 5, 1, 1, 1, 1, 1, 1, 6, 6, 27, 28, 28, 28, 28, 1, 1, 1, 1, 32, 32, 32, 32, 32, 5, 1, 1, 27, 1, 1, 2, 2, 2] 78 rigid atoms, others: [32, 34, 35, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 33, 36, 37, 38]) total number of confs: 120 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074654 none C[C@@H]1C[C@H]1C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 13, 13, 13, 32, 32, 32, 32, 67, 67, 78, 78, 78, 78, 78, 32, 32, 32, 32, 2, 2, 2, 1, 1, 13, 32, 32, 78, 32, 32, 32, 32, 32] 78 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 218 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.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: REAL250005074654 none C[C@@H]1C[C@H]1C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 46, 78, 46, 46, 27, 27, 27, 27, 9, 1, 9, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 78, 78, 78, 78, 78, 46, 27, 27, 1, 27, 27, 28, 28, 28] 78 rigid atoms, others: [33, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38]) total number of confs: 223 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074654 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074654 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074654/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074654 Building REAL250005074655 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074655' /scratch/stefan/7916156/working/building/REAL250005074655 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074655 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074655/0 /scratch/stefan/7916156/working/building/REAL250005074655 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 775) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/775 `/scratch/stefan/7916156/working/3D/775' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(F)C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005074655.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074655/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074655 none CCC(F)C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [121, 120, 63, 120, 63, 63, 30, 30, 30, 30, 9, 1, 9, 1, 1, 1, 1, 1, 1, 29, 29, 30, 29, 121, 121, 121, 121, 121, 120, 63, 30, 30, 1, 29, 29, 30, 30, 30] 121 rigid atoms, others: [32, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37]) total number of confs: 432 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074655 none CCC(F)C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [47, 34, 5, 34, 5, 5, 1, 1, 1, 1, 1, 1, 6, 6, 29, 29, 29, 30, 30, 1, 1, 1, 1, 55, 55, 55, 55, 55, 34, 5, 1, 1, 29, 1, 1, 2, 2, 2] 121 rigid atoms, others: [33, 34, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 32, 35, 36, 37]) total number of confs: 318 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074655 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074655 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074655/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074655 Building REAL250005074656 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074656' /scratch/stefan/7916156/working/building/REAL250005074656 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074656 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074656/0 /scratch/stefan/7916156/working/building/REAL250005074656 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 776) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/776 `/scratch/stefan/7916156/working/3D/776' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)CCCF) `REAL250005074656.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074656/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074656 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)CCCF NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 184 conformations in input total number of sets (complete confs): 184 using faster count positions algorithm for large data unique positions, atoms: [24, 25, 25, 24, 6, 1, 6, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 63, 63, 63, 166, 169, 184, 25, 25, 25, 25, 25, 1, 25, 25, 63, 166, 166, 184, 184, 184, 184] 184 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 802 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074656 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)CCCF NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 184 conformations in input total number of sets (complete confs): 184 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 24, 25, 25, 25, 25, 1, 1, 1, 1, 5, 5, 5, 30, 45, 100, 2, 2, 2, 1, 1, 24, 1, 1, 5, 30, 30, 58, 58, 98, 96] 184 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 26, 27, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 530 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074656 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074656 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074656/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074656 Building REAL250005074657 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074657' /scratch/stefan/7916156/working/building/REAL250005074657 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074657 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074657/0 /scratch/stefan/7916156/working/building/REAL250005074657 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 777) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/777 `/scratch/stefan/7916156/working/3D/777' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@@H]1C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005074657.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074657/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074657 none C[C@H]1C[C@@H]1C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 36, 36, 5, 36, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 30, 30, 30, 30, 30, 1, 1, 1, 1, 36, 36, 36, 36, 36, 5, 1, 1, 30, 1, 1, 2, 2, 2] 97 rigid atoms, others: [32, 34, 35, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 33, 36, 37, 38]) total number of confs: 130 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074657 none C[C@H]1C[C@@H]1C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 36, 36, 36, 36, 84, 84, 97, 97, 97, 97, 97, 36, 36, 36, 36, 2, 2, 2, 1, 1, 12, 36, 36, 97, 36, 36, 36, 36, 36] 97 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 262 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.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: REAL250005074657 none C[C@H]1C[C@@H]1C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 58, 97, 58, 58, 30, 30, 30, 30, 9, 1, 9, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 97, 97, 97, 97, 97, 58, 30, 30, 1, 30, 30, 30, 30, 30] 97 rigid atoms, others: [33, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38]) total number of confs: 278 number of broken/clashed sets: 5 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074657 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074657 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074657/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074657 Building REAL250005074658 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074658' /scratch/stefan/7916156/working/building/REAL250005074658 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074658 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074658/0 /scratch/stefan/7916156/working/building/REAL250005074658 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 778) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/778 `/scratch/stefan/7916156/working/3D/778' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C(N)=O) `REAL250005074658.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074658/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074658 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 10, 1, 10, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 39, 39, 39, 50, 50, 23, 23, 23, 23, 23, 1, 23, 23, 39, 50, 50] 50 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 27] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32]) total number of confs: 135 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074658 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 23, 23, 23, 23, 23, 1, 1, 1, 1, 5, 5, 5, 18, 18, 2, 2, 2, 1, 1, 23, 1, 1, 5, 18, 18] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 25, 26, 28, 29] set([32, 6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 27, 30, 31]) total number of confs: 85 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074658 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074658 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074658/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074658 Building REAL250005074659 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074659' /scratch/stefan/7916156/working/building/REAL250005074659 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074659 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074659/0 /scratch/stefan/7916156/working/building/REAL250005074659 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 779) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/779 `/scratch/stefan/7916156/working/3D/779' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C(C)(C)C) `REAL250005074659.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074659/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074659 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [20, 21, 21, 20, 8, 1, 8, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 29, 29, 29, 32, 32, 32, 21, 21, 21, 21, 21, 1, 21, 21, 29, 32, 32, 32, 32, 32, 32, 32, 32, 32] 32 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 98 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074659 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 20, 21, 21, 21, 21, 1, 1, 1, 1, 5, 5, 5, 8, 8, 8, 2, 2, 2, 1, 1, 20, 1, 1, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8] 32 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 26, 27, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 69 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074659 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074659 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074659/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074659 Building REAL250005074660 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074660' /scratch/stefan/7916156/working/building/REAL250005074660 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074660 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074660/0 /scratch/stefan/7916156/working/building/REAL250005074660 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 780) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/780 `/scratch/stefan/7916156/working/3D/780' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005074660.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074660/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074660 none C=CCC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [88, 88, 53, 53, 53, 29, 29, 29, 29, 10, 1, 10, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 88, 88, 88, 88, 88, 53, 29, 29, 1, 29, 29, 29, 29, 29] 88 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 310 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074660 none C=CCC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [49, 31, 5, 5, 5, 1, 1, 1, 1, 1, 1, 6, 7, 29, 29, 29, 29, 29, 1, 1, 1, 1, 49, 49, 49, 31, 31, 5, 1, 1, 29, 1, 1, 2, 2, 2] 88 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 28, 29, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 30, 33, 34, 35]) total number of confs: 212 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074660 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074660 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074660/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074660 Building REAL250005074661 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074661' /scratch/stefan/7916156/working/building/REAL250005074661 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005074661 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074661/0 /scratch/stefan/7916156/working/building/REAL250005074661 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 781) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/781 `/scratch/stefan/7916156/working/3D/781' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C[NH+](C)C) `REAL250005074661.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074661/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074661 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 8, 8, 8, 8, 8, 8, 8, 6, 6, 6, 5, 5, 1, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8] 8 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 19 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074661 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 2, 5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 4, 4, 5, 6, 6, 6, 2, 2, 2, 1, 1, 5, 1, 1, 4, 5, 5, 6, 6, 6, 6, 6, 6] 8 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 27, 28, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 36 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074661 /scratch/stefan/7916156/working /scratch/stefan/7916156 mkdir: created directory `1' /scratch/stefan/7916156/working/building/REAL250005074661/1 /scratch/stefan/7916156/working/building/REAL250005074661 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 1 (index: 782) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/782 `/scratch/stefan/7916156/working/3D/782' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)CN(C)C) `REAL250005074661.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005074661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074661/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074661 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)CN(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 21, 9, 1, 9, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 42, 42, 42, 77, 77, 77, 22, 22, 22, 21, 21, 1, 22, 22, 42, 77, 77, 77, 77, 77, 77, 77, 77] 77 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 275 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074661 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)CN(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 21, 21, 21, 21, 21, 1, 1, 1, 1, 4, 4, 4, 26, 29, 29, 2, 2, 2, 1, 1, 22, 1, 1, 4, 26, 26, 29, 29, 29, 29, 29, 29] 77 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 26, 27, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074661 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074661 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 1: /scratch/stefan/7916156/working/building/REAL250005074661/1.* 0: /scratch/stefan/7916156/working/building/REAL250005074661/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074661 Building REAL250005074662 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074662' /scratch/stefan/7916156/working/building/REAL250005074662 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074662 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074662/0 /scratch/stefan/7916156/working/building/REAL250005074662 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 783) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/783 `/scratch/stefan/7916156/working/3D/783' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(O)C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005074662.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074662.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074662/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074662 none C=CC(O)C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 258 conformations in input total number of sets (complete confs): 258 using faster count positions algorithm for large data unique positions, atoms: [86, 86, 56, 86, 56, 56, 26, 26, 26, 26, 9, 1, 9, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 86, 86, 86, 86, 258, 56, 26, 26, 1, 26, 26, 26, 26, 26] 258 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36]) total number of confs: 547 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074662 none C=CC(O)C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 258 conformations in input total number of sets (complete confs): 258 using faster count positions algorithm for large data unique positions, atoms: [55, 30, 5, 30, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 26, 26, 26, 26, 26, 1, 1, 1, 1, 55, 55, 55, 30, 90, 5, 1, 1, 26, 1, 1, 2, 2, 2] 258 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 31, 34, 35, 36]) total number of confs: 313 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074662 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074662 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074662/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074662 Building REAL250005074663 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074663' /scratch/stefan/7916156/working/building/REAL250005074663 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074663 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074663/0 /scratch/stefan/7916156/working/building/REAL250005074663 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 784) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/784 `/scratch/stefan/7916156/working/3D/784' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C1COC1) `REAL250005074663.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074663/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074663 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C1COC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 28, 9, 1, 9, 1, 1, 1, 1, 1, 1, 28, 29, 29, 29, 53, 53, 53, 80, 80, 80, 29, 29, 29, 28, 28, 1, 28, 28, 53, 80, 80, 80, 80, 80] 80 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 215 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074663 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C1COC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 28, 28, 29, 28, 28, 1, 1, 1, 1, 5, 5, 5, 29, 29, 29, 2, 2, 2, 1, 1, 28, 1, 1, 5, 29, 29, 29, 29, 29] 80 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 26, 27, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 31, 32, 33, 34, 35, 36]) total number of confs: 115 number of broken/clashed sets: 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.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: REAL250005074663 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C1COC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 29, 29, 29, 68, 68, 80, 80, 80, 80, 80, 29, 10, 29, 10, 1, 10, 1, 1, 1, 1, 29, 29, 29, 29, 29, 80, 29, 29, 10, 1, 1, 1, 1, 1] 80 rigid atoms, others: [32, 33, 34, 35, 36, 17, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 217 number of broken/clashed sets: 8 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074663 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074663 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074663/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074663 Building REAL250005074664 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074664' /scratch/stefan/7916156/working/building/REAL250005074664 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074664 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074664/0 /scratch/stefan/7916156/working/building/REAL250005074664 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 785) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/785 `/scratch/stefan/7916156/working/3D/785' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](C)C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005074664.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074664/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074664 none CO[C@H](C)C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 42, 57, 57, 42, 42, 22, 22, 22, 22, 10, 1, 10, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 57, 57, 57, 57, 57, 57, 42, 22, 22, 1, 22, 22, 22, 22, 22] 57 rigid atoms, others: [33, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38]) total number of confs: 183 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074664 none CO[C@H](C)C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [29, 23, 5, 23, 23, 5, 5, 1, 1, 1, 1, 1, 1, 6, 6, 22, 22, 22, 22, 22, 1, 1, 1, 1, 29, 29, 29, 23, 23, 23, 5, 1, 1, 22, 1, 1, 2, 2, 2] 57 rigid atoms, others: [32, 34, 35, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 33, 36, 37, 38]) total number of confs: 125 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074664 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074664 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074664/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074664 Building REAL250005074665 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074665' /scratch/stefan/7916156/working/building/REAL250005074665 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074665 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074665/0 /scratch/stefan/7916156/working/building/REAL250005074665 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 786) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/786 `/scratch/stefan/7916156/working/3D/786' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC=CC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005074665.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074665/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074665 none CCC=CC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 110 conformations in input total number of sets (complete confs): 110 using faster count positions algorithm for large data unique positions, atoms: [110, 91, 91, 58, 58, 58, 29, 29, 29, 29, 9, 1, 9, 1, 1, 1, 1, 1, 1, 28, 28, 29, 29, 110, 110, 110, 110, 110, 91, 91, 58, 29, 29, 1, 29, 29, 29, 29, 29] 110 rigid atoms, others: [33, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38]) total number of confs: 389 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074665 none CCC=CC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 110 conformations in input total number of sets (complete confs): 110 using faster count positions algorithm for large data unique positions, atoms: [51, 30, 30, 5, 5, 5, 1, 1, 1, 1, 1, 1, 6, 6, 28, 29, 29, 29, 29, 1, 1, 1, 1, 51, 51, 51, 51, 51, 30, 30, 5, 1, 1, 28, 1, 1, 2, 2, 2] 110 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 33, 36, 37, 38]) total number of confs: 234 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074665 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074665 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074665/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074665 Building REAL250005074666 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074666' /scratch/stefan/7916156/working/building/REAL250005074666 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074666 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074666/0 /scratch/stefan/7916156/working/building/REAL250005074666 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 787) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/787 `/scratch/stefan/7916156/working/3D/787' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)CN=[N+]=[N-]) `REAL250005074666.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074666/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074666 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)CN=[N+]=[N-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.2', 'N.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 30, 30, 10, 1, 10, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 62, 62, 62, 182, 201, 201, 30, 30, 30, 30, 30, 1, 30, 30, 62, 182, 182] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33]) total number of confs: 679 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074666 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)CN=[N+]=[N-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.2', 'N.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 30, 30, 30, 30, 30, 1, 1, 1, 1, 5, 5, 5, 43, 132, 132, 2, 2, 2, 1, 1, 30, 1, 1, 5, 43, 43] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 26, 27, 29, 30] set([32, 33, 6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 31]) total number of confs: 307 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074666 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074666 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074666/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074666 Building REAL250005074667 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074667' /scratch/stefan/7916156/working/building/REAL250005074667 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074667 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074667/0 /scratch/stefan/7916156/working/building/REAL250005074667 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 788) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/788 `/scratch/stefan/7916156/working/3D/788' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)CO) `REAL250005074667.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074667/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074667 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 25, 25, 10, 1, 10, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 32, 32, 32, 34, 25, 25, 25, 25, 25, 1, 25, 25, 32, 34, 34, 102] 102 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 26] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32]) total number of confs: 181 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074667 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 25, 25, 25, 25, 25, 1, 1, 1, 1, 4, 4, 4, 19, 2, 2, 2, 1, 1, 25, 1, 1, 4, 19, 19, 57] 102 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 24, 25, 27, 28] set([32, 6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 26, 29, 30, 31]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074667 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074667 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074667/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074667 Building REAL250005074668 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074668' /scratch/stefan/7916156/working/building/REAL250005074668 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074668 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074668/0 /scratch/stefan/7916156/working/building/REAL250005074668 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 789) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/789 `/scratch/stefan/7916156/working/3D/789' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005074668.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074668/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074668 none CC(O)C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [49, 38, 49, 38, 38, 23, 23, 23, 23, 9, 1, 9, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 49, 49, 49, 49, 147, 38, 23, 23, 1, 23, 23, 23, 23, 23] 147 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 296 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074668 none CC(O)C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [29, 5, 29, 5, 5, 1, 1, 1, 1, 1, 1, 6, 6, 23, 23, 23, 23, 23, 1, 1, 1, 1, 29, 29, 29, 29, 87, 5, 1, 1, 23, 1, 1, 2, 2, 2] 147 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 28, 29, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 30, 33, 34, 35]) total number of confs: 222 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074668 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074668 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074668/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074668 Building REAL250005074669 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074669' /scratch/stefan/7916156/working/building/REAL250005074669 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074669 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074669/0 /scratch/stefan/7916156/working/building/REAL250005074669 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 790) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/790 `/scratch/stefan/7916156/working/3D/790' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C1CC1F) `REAL250005074669.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074669/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074669 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C1CC1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 28, 9, 1, 9, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 61, 61, 61, 96, 96, 96, 28, 28, 28, 28, 28, 1, 28, 28, 61, 96, 96, 96, 96] 96 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 270 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074669 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C1CC1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 7, 7, 28, 28, 28, 28, 28, 1, 1, 1, 1, 5, 5, 5, 36, 36, 36, 2, 2, 2, 1, 1, 28, 1, 1, 5, 36, 36, 36, 36] 96 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 26, 27, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 31, 32, 33, 34, 35]) total number of confs: 128 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.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: REAL250005074669 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C1CC1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 36, 36, 36, 36, 85, 85, 96, 96, 96, 96, 96, 36, 13, 36, 13, 1, 13, 1, 1, 1, 1, 36, 36, 36, 36, 36, 96, 36, 36, 13, 1, 1, 1, 1] 96 rigid atoms, others: [32, 33, 34, 35, 17, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 261 number of broken/clashed sets: 5 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074669 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074669 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074669/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074669 Building REAL250005074670 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074670' /scratch/stefan/7916156/working/building/REAL250005074670 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074670 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074670/0 /scratch/stefan/7916156/working/building/REAL250005074670 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 791) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/791 `/scratch/stefan/7916156/working/3D/791' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)CCF) `REAL250005074670.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074670.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074670/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074670 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)CCF NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 26, 8, 1, 8, 1, 1, 1, 1, 1, 1, 26, 27, 27, 27, 52, 52, 52, 108, 108, 27, 27, 27, 26, 26, 1, 27, 27, 52, 108, 108, 108, 108] 108 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 27] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 390 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074670 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)CCF NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 26, 26, 26, 26, 26, 1, 1, 1, 1, 5, 5, 5, 31, 54, 2, 2, 2, 1, 1, 26, 1, 1, 5, 31, 31, 54, 54] 108 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 25, 26, 28, 29] set([32, 33, 34, 6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 27, 30, 31]) total number of confs: 268 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074670 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074670 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074670/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074670 Building REAL250005074671 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074671' /scratch/stefan/7916156/working/building/REAL250005074671 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074671 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074671/0 /scratch/stefan/7916156/working/building/REAL250005074671 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 792) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/792 `/scratch/stefan/7916156/working/3D/792' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C=CCF) `REAL250005074671.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074671/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074671 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C=CCF NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 1, 1, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 26, 25, 9, 1, 9, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 46, 46, 46, 75, 75, 81, 26, 26, 26, 25, 25, 1, 26, 26, 46, 75, 75, 81, 81] 81 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 250 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074671 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C=CCF NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 1, 1, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 25, 25, 25, 26, 26, 1, 1, 1, 1, 5, 5, 5, 21, 21, 49, 2, 2, 2, 1, 1, 25, 1, 1, 5, 21, 21, 49, 49] 81 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 26, 27, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 31, 32, 33, 34, 35]) total number of confs: 212 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074671 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074671 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074671/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074671 Building REAL250005074672 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074672' /scratch/stefan/7916156/working/building/REAL250005074672 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074672 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074672/0 /scratch/stefan/7916156/working/building/REAL250005074672 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 793) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/793 `/scratch/stefan/7916156/working/3D/793' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005074672.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074672/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074672 none C#CCCC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 134 conformations in input total number of sets (complete confs): 134 using faster count positions algorithm for large data unique positions, atoms: [134, 134, 125, 64, 64, 64, 30, 30, 30, 30, 8, 1, 8, 1, 1, 1, 1, 1, 1, 29, 29, 30, 29, 134, 134, 134, 125, 125, 64, 30, 30, 1, 30, 30, 30, 30, 30] 134 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36]) total number of confs: 505 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074672 none C#CCCC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 134 conformations in input total number of sets (complete confs): 134 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 30, 5, 5, 5, 1, 1, 1, 1, 1, 1, 6, 6, 29, 30, 30, 30, 30, 1, 1, 1, 1, 56, 56, 56, 30, 30, 5, 1, 1, 29, 1, 1, 2, 2, 2] 134 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 31, 34, 35, 36]) total number of confs: 285 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074672 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074672 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074672/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074672 Building REAL250005074673 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074673' /scratch/stefan/7916156/working/building/REAL250005074673 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074673 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074673/0 /scratch/stefan/7916156/working/building/REAL250005074673 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 794) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/794 `/scratch/stefan/7916156/working/3D/794' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C1CCO1) `REAL250005074673.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074673/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074673 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C1CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 10, 1, 10, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 34, 34, 34, 44, 44, 44, 23, 23, 23, 23, 23, 1, 23, 23, 34, 44, 44, 44, 44, 44] 44 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 117 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074673 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C1CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 23, 23, 23, 23, 23, 1, 1, 1, 1, 5, 5, 5, 25, 25, 25, 2, 2, 2, 1, 1, 23, 1, 1, 5, 25, 25, 25, 25, 25] 44 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 26, 27, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 31, 32, 33, 34, 35, 36]) total number of confs: 99 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.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: REAL250005074673 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C1CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 25, 25, 41, 41, 44, 44, 44, 44, 44, 25, 10, 25, 10, 1, 10, 1, 1, 1, 1, 25, 25, 25, 25, 25, 44, 25, 25, 10, 1, 1, 1, 1, 1] 44 rigid atoms, others: [32, 33, 34, 35, 36, 17, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 127 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074673 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074673 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074673/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074673 Building REAL250005074674 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074674' /scratch/stefan/7916156/working/building/REAL250005074674 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074674 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074674/0 /scratch/stefan/7916156/working/building/REAL250005074674 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 795) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/795 `/scratch/stefan/7916156/working/3D/795' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C(C)(C)O) `REAL250005074674.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074674/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074674 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C(C)(C)O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 20, 9, 1, 9, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 41, 41, 41, 67, 67, 67, 21, 21, 21, 20, 20, 1, 21, 21, 41, 67, 67, 67, 67, 67, 67, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 441 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074674 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C(C)(C)O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 20, 20, 20, 20, 20, 1, 1, 1, 1, 5, 5, 5, 24, 24, 24, 2, 2, 2, 1, 1, 21, 1, 1, 5, 24, 24, 24, 24, 24, 24, 72] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 26, 27, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 190 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074674 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074674 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074674/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074674 Building REAL250005074675 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074675' /scratch/stefan/7916156/working/building/REAL250005074675 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074675 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074675/0 /scratch/stefan/7916156/working/building/REAL250005074675 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 796) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/796 `/scratch/stefan/7916156/working/3D/796' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC1C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005074675.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074675/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074675 none CC1=CC1C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 104 conformations in input total number of sets (complete confs): 104 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 39, 5, 5, 5, 1, 1, 1, 1, 1, 1, 6, 6, 25, 26, 26, 25, 25, 1, 1, 1, 1, 39, 39, 39, 39, 39, 5, 1, 1, 26, 1, 1, 2, 2, 2] 104 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 31, 34, 35, 36]) total number of confs: 135 number of broken/clashed sets: 11 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074675 none CC1=CC1C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 13, 13, 13, 39, 39, 39, 39, 80, 80, 104, 104, 104, 104, 104, 39, 39, 39, 39, 2, 2, 2, 1, 1, 13, 39, 39, 104, 39, 39, 39, 39, 39] 104 rigid atoms, others: [0, 1, 2, 3, 4, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 272 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.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: REAL250005074675 none CC1=CC1C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 48, 48, 48, 26, 26, 26, 25, 9, 1, 9, 1, 1, 1, 1, 1, 1, 25, 26, 26, 26, 104, 104, 104, 104, 104, 48, 25, 25, 1, 26, 26, 26, 26, 26] 104 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36]) total number of confs: 286 number of broken/clashed sets: 11 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074675 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074675 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074675/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074675 Building REAL250005074676 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074676' /scratch/stefan/7916156/working/building/REAL250005074676 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074676 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074676/0 /scratch/stefan/7916156/working/building/REAL250005074676 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 797) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/797 `/scratch/stefan/7916156/working/3D/797' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005074676.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074676/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074676 none C[C@@H](O)C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 159 conformations in input total number of sets (complete confs): 159 using faster count positions algorithm for large data unique positions, atoms: [53, 45, 53, 53, 45, 45, 30, 30, 30, 30, 10, 1, 10, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 53, 53, 53, 159, 45, 30, 30, 1, 30, 30, 30, 30, 30] 159 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 306 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074676 none C[C@@H](O)C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 159 conformations in input total number of sets (complete confs): 159 using faster count positions algorithm for large data unique positions, atoms: [26, 5, 26, 26, 5, 5, 1, 1, 1, 1, 1, 1, 6, 6, 30, 30, 30, 30, 30, 1, 1, 1, 1, 26, 26, 26, 78, 5, 1, 1, 30, 1, 1, 2, 2, 2] 159 rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 28, 29, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 30, 33, 34, 35]) total number of confs: 212 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074676 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074676 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074676/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074676 Building REAL250005074677 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074677' /scratch/stefan/7916156/working/building/REAL250005074677 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074677 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074677/0 /scratch/stefan/7916156/working/building/REAL250005074677 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 798) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/798 `/scratch/stefan/7916156/working/3D/798' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C=CCO) `REAL250005074677.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074677/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074677 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C=CCO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 1, 1, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 297 conformations in input total number of sets (complete confs): 297 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 27, 8, 1, 8, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 58, 58, 58, 96, 96, 99, 28, 28, 28, 27, 27, 1, 28, 28, 58, 96, 96, 99, 99, 297] 297 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 581 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074677 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C=CCO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 1, 1, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 297 conformations in input total number of sets (complete confs): 297 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 27, 27, 27, 27, 27, 1, 1, 1, 1, 5, 5, 5, 24, 24, 63, 2, 2, 2, 1, 1, 28, 1, 1, 5, 24, 24, 63, 63, 189] 297 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 26, 27, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 31, 32, 33, 34, 35, 36]) total number of confs: 455 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074677 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074677 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074677/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074677 Building REAL250005074678 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074678' /scratch/stefan/7916156/working/building/REAL250005074678 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074678 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074678/0 /scratch/stefan/7916156/working/building/REAL250005074678 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 799) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/799 `/scratch/stefan/7916156/working/3D/799' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C1=CCC1) `REAL250005074678.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074678.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074678/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074678 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C1=CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 9, 1, 9, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 29, 29, 29, 29, 29, 29, 20, 20, 20, 20, 20, 1, 20, 20, 29, 29, 29, 29, 29, 29] 29 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 70 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074678 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C1=CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 20, 20, 20, 20, 20, 1, 1, 1, 1, 5, 5, 5, 12, 12, 12, 2, 2, 2, 1, 1, 20, 1, 1, 5, 12, 12, 12, 12, 12] 29 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 26, 27, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 31, 32, 33, 34, 35, 36]) total number of confs: 60 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.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: REAL250005074678 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C1=CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 12, 12, 22, 22, 29, 29, 29, 29, 29, 12, 7, 12, 7, 1, 7, 1, 1, 1, 1, 12, 12, 12, 12, 12, 29, 12, 12, 7, 1, 1, 1, 1, 1] 29 rigid atoms, others: [32, 33, 34, 35, 36, 17, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 74 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074678 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074678 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074678/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074678 Building REAL250005074679 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074679' /scratch/stefan/7916156/working/building/REAL250005074679 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074679 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074679/0 /scratch/stefan/7916156/working/building/REAL250005074679 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 800) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/800 `/scratch/stefan/7916156/working/3D/800' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CON=CC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005074679.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074679/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074679 none CON=CC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 8, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 31, 31, 31, 20, 20, 20, 20, 8, 1, 8, 1, 1, 1, 1, 1, 1, 19, 19, 20, 20, 39, 39, 39, 39, 31, 20, 20, 1, 20, 20, 20, 20, 20] 39 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 112 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074679 none CON=CC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 8, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [24, 17, 17, 5, 5, 5, 1, 1, 1, 1, 1, 1, 6, 7, 19, 20, 20, 20, 20, 1, 1, 1, 1, 24, 24, 24, 17, 5, 1, 1, 19, 1, 1, 2, 2, 2] 39 rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 28, 29, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 30, 33, 34, 35]) total number of confs: 92 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074679 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074679 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074679/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074679 Building REAL250005074680 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074680' /scratch/stefan/7916156/working/building/REAL250005074680 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074680 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074680/0 /scratch/stefan/7916156/working/building/REAL250005074680 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 801) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/801 `/scratch/stefan/7916156/working/3D/801' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C1(F)CC1) `REAL250005074680.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074680.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074680/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074680 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C1(F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 30, 30, 10, 1, 10, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 61, 61, 61, 82, 82, 82, 30, 30, 30, 30, 30, 1, 30, 30, 61, 82, 82, 82, 82] 82 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 226 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074680 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C1(F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 30, 30, 30, 30, 30, 1, 1, 1, 1, 5, 5, 5, 31, 31, 31, 2, 2, 2, 1, 1, 30, 1, 1, 5, 31, 31, 31, 31] 82 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 26, 27, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 31, 32, 33, 34, 35]) total number of confs: 119 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.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: REAL250005074680 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C1(F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 31, 31, 31, 31, 68, 68, 82, 82, 82, 82, 82, 31, 13, 31, 13, 1, 13, 1, 1, 1, 1, 31, 31, 31, 31, 31, 82, 31, 31, 13, 1, 1, 1, 1] 82 rigid atoms, others: [32, 33, 34, 35, 17, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 222 number of broken/clashed sets: 5 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074680 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074680 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074680/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074680 Building REAL250005074681 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074681' /scratch/stefan/7916156/working/building/REAL250005074681 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074681 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074681/0 /scratch/stefan/7916156/working/building/REAL250005074681 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 802) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/802 `/scratch/stefan/7916156/working/3D/802' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=C(F)C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005074681.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074681.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074681/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074681 none CC=C(F)C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 36, 46, 36, 36, 23, 23, 23, 23, 9, 1, 9, 1, 1, 1, 1, 1, 1, 22, 22, 23, 23, 46, 46, 46, 46, 36, 23, 23, 1, 23, 23, 23, 23, 23] 46 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 130 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074681 none CC=C(F)C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 5, 20, 5, 5, 1, 1, 1, 1, 1, 1, 6, 7, 22, 23, 23, 23, 23, 1, 1, 1, 1, 21, 21, 21, 21, 5, 1, 1, 22, 1, 1, 2, 2, 2] 46 rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 28, 29, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 30, 33, 34, 35]) total number of confs: 92 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074681 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074681 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074681/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074681 Building REAL250005074682 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074682' /scratch/stefan/7916156/working/building/REAL250005074682 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074682 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074682/0 /scratch/stefan/7916156/working/building/REAL250005074682 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 803) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/803 `/scratch/stefan/7916156/working/3D/803' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CO)C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005074682.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074682/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074682 none CC(CO)C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 369 conformations in input total number of sets (complete confs): 369 using faster count positions algorithm for large data unique positions, atoms: [119, 56, 119, 123, 56, 56, 27, 27, 27, 27, 10, 1, 10, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 119, 119, 119, 119, 123, 123, 369, 56, 27, 27, 1, 27, 27, 27, 27, 27] 369 rigid atoms, others: [33, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38]) total number of confs: 833 number of broken/clashed sets: 48 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074682 none CC(CO)C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 369 conformations in input total number of sets (complete confs): 369 using faster count positions algorithm for large data unique positions, atoms: [29, 5, 29, 60, 5, 5, 1, 1, 1, 1, 1, 1, 6, 7, 27, 26, 27, 27, 27, 1, 1, 1, 1, 29, 29, 29, 29, 60, 60, 180, 5, 1, 1, 27, 1, 1, 2, 2, 2] 369 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 33, 36, 37, 38]) total number of confs: 458 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074682 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074682 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074682/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074682 Building REAL250005074683 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074683' /scratch/stefan/7916156/working/building/REAL250005074683 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074683 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074683/0 /scratch/stefan/7916156/working/building/REAL250005074683 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 804) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/804 `/scratch/stefan/7916156/working/3D/804' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005074683.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074683/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074683 none C[C@H](O)C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 40, 50, 50, 40, 40, 25, 25, 25, 25, 9, 1, 9, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 50, 50, 50, 150, 40, 25, 25, 1, 25, 25, 25, 25, 25] 150 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 301 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074683 none C[C@H](O)C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [24, 5, 24, 24, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 25, 25, 25, 25, 25, 1, 1, 1, 1, 24, 24, 24, 72, 5, 1, 1, 25, 1, 1, 2, 2, 2] 150 rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 28, 29, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 30, 33, 34, 35]) total number of confs: 196 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074683 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074683 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074683/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074683 Building REAL250005074684 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074684' /scratch/stefan/7916156/working/building/REAL250005074684 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074684 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074684/0 /scratch/stefan/7916156/working/building/REAL250005074684 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 805) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/805 `/scratch/stefan/7916156/working/3D/805' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C1CC1C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005074684.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074684/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074684 none C=C1CC1C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 38, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 30, 30, 30, 30, 30, 1, 1, 1, 1, 38, 38, 38, 38, 38, 5, 1, 1, 30, 1, 1, 2, 2, 2] 94 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 31, 34, 35, 36]) total number of confs: 134 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074684 none C=C1CC1C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 13, 13, 13, 38, 38, 38, 38, 78, 78, 94, 94, 94, 94, 94, 38, 38, 38, 38, 1, 1, 1, 1, 1, 13, 38, 38, 94, 38, 38, 38, 38, 38] 94 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 25, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 251 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.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: REAL250005074684 none C=C1CC1C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [94, 94, 94, 47, 47, 47, 30, 30, 30, 30, 10, 1, 10, 1, 1, 1, 1, 1, 1, 29, 30, 30, 30, 94, 94, 94, 94, 94, 47, 30, 30, 1, 30, 30, 30, 30, 30] 94 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36]) total number of confs: 260 number of broken/clashed sets: 10 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074684 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074684 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074684/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074684 Building REAL250005074685 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074685' /scratch/stefan/7916156/working/building/REAL250005074685 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074685 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074685/0 /scratch/stefan/7916156/working/building/REAL250005074685 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 806) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/806 `/scratch/stefan/7916156/working/3D/806' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CF)C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005074685.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074685/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074685 none CC(CF)C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [122, 58, 122, 125, 58, 58, 24, 24, 24, 24, 10, 1, 10, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 122, 122, 122, 122, 125, 125, 58, 24, 24, 1, 24, 24, 24, 24, 24] 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, 33, 34, 35, 36, 37]) total number of confs: 445 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074685 none CC(CF)C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [35, 5, 35, 67, 5, 5, 1, 1, 1, 1, 1, 1, 6, 6, 24, 24, 24, 24, 24, 1, 1, 1, 1, 35, 35, 35, 35, 67, 67, 5, 1, 1, 24, 1, 1, 2, 2, 2] 125 rigid atoms, others: [33, 34, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 32, 35, 36, 37]) total number of confs: 307 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074685 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074685 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074685/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074685 Building REAL250005074686 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074686' /scratch/stefan/7916156/working/building/REAL250005074686 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074686 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074686/0 /scratch/stefan/7916156/working/building/REAL250005074686 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 807) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/807 `/scratch/stefan/7916156/working/3D/807' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)CC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005074686.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074686/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074686 none C=C(C)CC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [108, 108, 108, 56, 56, 56, 29, 29, 29, 29, 10, 1, 10, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 108, 108, 108, 108, 108, 108, 108, 56, 29, 29, 1, 29, 29, 29, 29, 29] 108 rigid atoms, others: [33, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38]) total number of confs: 383 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074686 none C=C(C)CC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [55, 38, 55, 5, 5, 5, 1, 1, 1, 1, 1, 1, 6, 6, 29, 29, 29, 29, 29, 1, 1, 1, 1, 55, 55, 55, 55, 55, 38, 38, 5, 1, 1, 29, 1, 1, 2, 2, 2] 108 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 33, 36, 37, 38]) total number of confs: 231 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074686 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074686 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074686/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074686 Building REAL250005074687 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074687' /scratch/stefan/7916156/working/building/REAL250005074687 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074687 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074687/0 /scratch/stefan/7916156/working/building/REAL250005074687 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 808) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/808 `/scratch/stefan/7916156/working/3D/808' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005074687.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074687.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074687/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074687 none CC=CC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 32, 32, 32, 22, 22, 22, 22, 8, 1, 8, 1, 1, 1, 1, 1, 1, 21, 21, 22, 22, 42, 42, 42, 42, 42, 32, 22, 22, 1, 22, 22, 22, 22, 22] 42 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 126 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074687 none CC=CC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 5, 5, 5, 1, 1, 1, 1, 1, 1, 6, 7, 21, 22, 22, 22, 22, 1, 1, 1, 1, 20, 20, 20, 20, 20, 5, 1, 1, 21, 1, 1, 2, 2, 2] 42 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 28, 29, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 30, 33, 34, 35]) total number of confs: 88 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074687 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074687 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074687/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074687 Building REAL250005074688 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074688' /scratch/stefan/7916156/working/building/REAL250005074688 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074688 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074688/0 /scratch/stefan/7916156/working/building/REAL250005074688 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 809) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/809 `/scratch/stefan/7916156/working/3D/809' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H]1C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005074688.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074688/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074688 none C[C@@H]1C[C@H]1C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 32, 32, 5, 32, 5, 5, 1, 1, 1, 1, 1, 1, 6, 6, 27, 28, 28, 28, 28, 1, 1, 1, 1, 32, 32, 32, 32, 32, 5, 1, 1, 27, 1, 1, 2, 2, 2] 78 rigid atoms, others: [32, 34, 35, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 33, 36, 37, 38]) total number of confs: 120 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074688 none C[C@@H]1C[C@H]1C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 13, 13, 13, 32, 32, 32, 32, 67, 67, 78, 78, 78, 78, 78, 32, 32, 32, 32, 2, 2, 2, 1, 1, 13, 32, 32, 78, 32, 32, 32, 32, 32] 78 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 218 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.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: REAL250005074688 none C[C@@H]1C[C@H]1C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 46, 78, 46, 46, 27, 27, 27, 27, 9, 1, 9, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 78, 78, 78, 78, 78, 46, 27, 27, 1, 27, 27, 28, 28, 28] 78 rigid atoms, others: [33, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38]) total number of confs: 223 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074688 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074688 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074688/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074688 Building REAL250005074689 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074689' /scratch/stefan/7916156/working/building/REAL250005074689 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074689 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074689/0 /scratch/stefan/7916156/working/building/REAL250005074689 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 810) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/810 `/scratch/stefan/7916156/working/3D/810' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C1(O)CC1) `REAL250005074689.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074689/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074689 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C1(O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 219 conformations in input total number of sets (complete confs): 219 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 30, 30, 10, 1, 10, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 61, 61, 61, 73, 73, 73, 30, 30, 30, 30, 30, 1, 30, 30, 61, 219, 73, 73, 73, 73] 219 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 419 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074689 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C1(O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 219 conformations in input total number of sets (complete confs): 219 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 30, 30, 30, 30, 30, 1, 1, 1, 1, 5, 5, 5, 30, 30, 30, 2, 2, 2, 1, 1, 30, 1, 1, 5, 90, 30, 30, 30, 30] 219 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 26, 27, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 31, 32, 33, 34, 35, 36]) total number of confs: 207 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.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: REAL250005074689 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C1(O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 219 conformations in input total number of sets (complete confs): 219 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 30, 30, 30, 30, 61, 61, 73, 73, 73, 73, 73, 30, 11, 30, 11, 1, 11, 1, 1, 1, 1, 30, 30, 30, 30, 30, 73, 30, 30, 11, 6, 1, 1, 1, 1] 219 rigid atoms, others: [33, 34, 35, 36, 17, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 210 number of broken/clashed sets: 9 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074689 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074689 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074689/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074689 Building REAL250005074690 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074690' /scratch/stefan/7916156/working/building/REAL250005074690 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074690 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074690/0 /scratch/stefan/7916156/working/building/REAL250005074690 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 811) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/811 `/scratch/stefan/7916156/working/3D/811' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)CC2CC2)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005074690.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074690/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074690 none C[C@@H]1CN(C(=O)CC2CC2)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [42, 42, 42, 42, 17, 3, 17, 1, 1, 1, 1, 42, 42, 42, 42, 65, 65, 65, 76, 76, 76, 76, 76, 42, 42, 42, 42, 42, 3, 3, 1, 1, 1, 1, 1, 42, 42, 65, 76] 76 rigid atoms, others: [32, 33, 34, 7, 8, 9, 10, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38]) total number of confs: 192 number of broken/clashed sets: 14 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074690 none C[C@@H]1CN(C(=O)CC2CC2)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 30, 42, 42, 1, 1, 1, 1, 5, 5, 5, 14, 14, 14, 14, 14, 2, 2, 2, 1, 1, 30, 30, 42, 42, 42, 42, 42, 1, 1, 5, 14] 76 rigid atoms, others: [0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 35, 36, 26, 27] set([6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 37, 38]) total number of confs: 178 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.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: REAL250005074690 none C[C@@H]1CN(C(=O)CC2CC2)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [14, 14, 14, 14, 14, 14, 35, 35, 70, 76, 76, 14, 7, 14, 7, 1, 7, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 70, 70, 76, 76, 76, 76, 76, 14, 14, 7, 1] 76 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: 294 number of broken/clashed sets: 14 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074690 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074690 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074690/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074690 Building REAL250005074691 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074691' /scratch/stefan/7916156/working/building/REAL250005074691 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074691 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074691/0 /scratch/stefan/7916156/working/building/REAL250005074691 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 812) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/812 `/scratch/stefan/7916156/working/3D/812' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C(C)(C)F)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005074691.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074691.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074691/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074691 none C[C@@H]1CN(C(=O)C(C)(C)F)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 15, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 9, 9, 16, 16, 23, 23, 23, 9, 6, 9, 6, 1, 6, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 23, 23, 23, 23, 23, 23, 9, 9, 6, 1] 23 rigid atoms, others: [37, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 89 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074691 none C[C@@H]1CN(C(=O)C(C)(C)F)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 15, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 17, 17, 17, 1, 1, 1, 1, 5, 5, 5, 9, 9, 9, 9, 9, 2, 2, 2, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1, 5, 9] 23 rigid atoms, others: [0, 1, 2, 3, 4, 5, 11, 12, 34, 14, 13, 35, 26, 27] set([6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 36, 37]) total number of confs: 86 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074691 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074691 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074691/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074691 Building REAL250005074692 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074692' /scratch/stefan/7916156/working/building/REAL250005074692 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074692 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074692/0 /scratch/stefan/7916156/working/building/REAL250005074692 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 813) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/813 `/scratch/stefan/7916156/working/3D/813' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074692.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074692/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074692 none COCC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [39, 38, 21, 9, 21, 9, 9, 9, 9, 9, 4, 9, 4, 1, 4, 1, 1, 1, 1, 1, 1, 9, 39, 39, 39, 38, 38, 9, 9, 9, 9, 9, 4, 1, 9, 9] 39 rigid atoms, others: [33, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35]) total number of confs: 145 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074692 none COCC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [28, 14, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 9, 9, 9, 9, 1, 29, 29, 29, 14, 14, 1, 1, 2, 2, 2, 5, 9, 1, 1] 39 rigid atoms, others: [34, 3, 5, 6, 7, 8, 9, 10, 11, 12, 35, 21, 27, 28] set([0, 1, 2, 4, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 100 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074692 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074692 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074692/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074692 Building REAL250005074693 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074693' /scratch/stefan/7916156/working/building/REAL250005074693 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074693 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074693/0 /scratch/stefan/7916156/working/building/REAL250005074693 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 814) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/814 `/scratch/stefan/7916156/working/3D/814' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074693.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074693/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074693 none CCCC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [53, 52, 31, 15, 31, 15, 15, 15, 15, 15, 7, 15, 7, 1, 7, 1, 1, 1, 1, 1, 1, 15, 53, 53, 53, 53, 53, 52, 52, 15, 15, 15, 15, 15, 7, 1, 15, 15] 53 rigid atoms, others: [35, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37]) total number of confs: 200 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074693 none CCCC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [31, 24, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 15, 15, 15, 1, 32, 32, 32, 31, 31, 24, 24, 1, 1, 2, 2, 2, 5, 15, 1, 1] 53 rigid atoms, others: [3, 36, 5, 6, 7, 8, 9, 10, 11, 12, 21, 29, 30, 37] set([0, 1, 2, 4, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35]) total number of confs: 163 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074693 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074693 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074693/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074693 Building REAL250005074694 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074694' /scratch/stefan/7916156/working/building/REAL250005074694 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074694 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074694/0 /scratch/stefan/7916156/working/building/REAL250005074694 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 815) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/815 `/scratch/stefan/7916156/working/3D/815' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074694.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074694/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074694 none CC(C)CC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [45, 46, 46, 28, 13, 28, 13, 13, 13, 13, 13, 7, 13, 7, 1, 7, 1, 1, 1, 1, 1, 1, 13, 46, 46, 46, 46, 46, 46, 46, 46, 46, 13, 13, 13, 13, 13, 8, 1, 13, 13] 46 rigid atoms, others: [38, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40]) total number of confs: 171 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074694 none CC(C)CC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [23, 22, 27, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 13, 13, 13, 13, 1, 27, 27, 27, 27, 27, 27, 27, 22, 22, 1, 1, 2, 2, 2, 5, 13, 1, 1] 46 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 11, 12, 13, 40, 22, 39] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38]) total number of confs: 157 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074694 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074694 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074694/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074694 Building REAL250005074695 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074695' /scratch/stefan/7916156/working/building/REAL250005074695 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074695 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074695/0 /scratch/stefan/7916156/working/building/REAL250005074695 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 816) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/816 `/scratch/stefan/7916156/working/3D/816' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC1C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074695.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074695/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074695 none CC1CC1C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 12, 12, 12, 12, 1, 15, 15, 15, 15, 15, 15, 15, 1, 1, 2, 2, 2, 5, 12, 1, 1] 23 rigid atoms, others: [4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 22, 38, 30, 31] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 66 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074695 none CC1CC1C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 6, 6, 15, 15, 15, 15, 15, 15, 15, 21, 21, 21, 23, 23, 23, 23, 23, 15, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 21, 23, 15, 15] 23 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 25, 26, 27, 28, 29] set([5, 6, 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: 51 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.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: REAL250005074695 none CC1CC1C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 18, 12, 18, 12, 12, 12, 12, 12, 7, 12, 7, 1, 7, 1, 1, 1, 1, 1, 1, 12, 23, 23, 23, 23, 23, 23, 23, 12, 12, 12, 12, 12, 7, 1, 12, 12] 23 rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 65 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074695 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074695 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074695/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074695 Building REAL250005074696 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074696' /scratch/stefan/7916156/working/building/REAL250005074696 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074696 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074696/0 /scratch/stefan/7916156/working/building/REAL250005074696 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 817) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/817 `/scratch/stefan/7916156/working/3D/817' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074696.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074696/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074696 none CCOCC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [102, 100, 87, 39, 16, 39, 16, 16, 16, 16, 16, 7, 16, 7, 1, 7, 1, 1, 1, 1, 1, 1, 16, 102, 102, 102, 102, 102, 87, 87, 16, 16, 16, 16, 16, 7, 1, 16, 16] 102 rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 347 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074696 none CCOCC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [86, 75, 35, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 16, 16, 16, 16, 16, 1, 86, 86, 86, 86, 86, 35, 35, 1, 1, 2, 2, 2, 5, 16, 1, 1] 102 rigid atoms, others: [4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 22, 38, 30, 31] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 272 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074696 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074696 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074696/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074696 Building REAL250005074697 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074697' /scratch/stefan/7916156/working/building/REAL250005074697 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074697 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074697/0 /scratch/stefan/7916156/working/building/REAL250005074697 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 818) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/818 `/scratch/stefan/7916156/working/3D/818' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)=CC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074697.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074697/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074697 none CC(C)=CC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 21, 11, 21, 11, 11, 11, 11, 11, 6, 11, 6, 1, 6, 1, 1, 1, 1, 1, 1, 11, 33, 33, 33, 33, 33, 33, 33, 11, 11, 11, 11, 11, 6, 1, 11, 11] 33 rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 109 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074697 none CC(C)=CC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 11, 11, 11, 11, 11, 1, 20, 20, 20, 20, 20, 20, 20, 1, 1, 2, 2, 2, 5, 11, 1, 1] 33 rigid atoms, others: [4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 22, 38, 30, 31] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 78 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074697 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074697 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074697/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074697 Building REAL250005074698 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074698' /scratch/stefan/7916156/working/building/REAL250005074698 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074698 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074698/0 /scratch/stefan/7916156/working/building/REAL250005074698 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 819) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/819 `/scratch/stefan/7916156/working/3D/819' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSCC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074698.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074698/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074698 none CSCC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [60, 47, 25, 11, 25, 11, 11, 11, 11, 11, 4, 11, 4, 1, 4, 1, 1, 1, 1, 1, 1, 11, 60, 60, 60, 47, 47, 11, 11, 11, 11, 11, 4, 1, 11, 11] 60 rigid atoms, others: [33, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35]) total number of confs: 203 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074698 none CSCC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [53, 26, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 11, 11, 11, 11, 11, 1, 53, 53, 53, 26, 26, 1, 1, 2, 2, 2, 5, 11, 1, 1] 60 rigid atoms, others: [34, 3, 5, 6, 7, 8, 9, 10, 11, 12, 35, 21, 27, 28] set([0, 1, 2, 4, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 153 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074698 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074698 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074698/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074698 Building REAL250005074699 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074699' /scratch/stefan/7916156/working/building/REAL250005074699 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074699 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074699/0 /scratch/stefan/7916156/working/building/REAL250005074699 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 820) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/820 `/scratch/stefan/7916156/working/3D/820' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074699.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074699.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074699/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074699 none CCCCC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [118, 113, 99, 44, 16, 44, 16, 16, 16, 16, 16, 7, 16, 7, 1, 7, 1, 1, 1, 1, 1, 1, 16, 118, 118, 118, 118, 118, 113, 113, 99, 99, 16, 16, 16, 16, 16, 7, 1, 16, 16] 118 rigid atoms, others: [38, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40]) total number of confs: 484 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074699 none CCCCC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [71, 49, 34, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 16, 16, 16, 16, 16, 1, 71, 72, 72, 70, 69, 53, 53, 35, 35, 1, 1, 2, 2, 2, 5, 16, 1, 1] 118 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 11, 12, 13, 40, 22, 39] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38]) total number of confs: 370 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074699 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074699 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074699/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074699 Building REAL250005074700 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074700' /scratch/stefan/7916156/working/building/REAL250005074700 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074700 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074700/0 /scratch/stefan/7916156/working/building/REAL250005074700 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 821) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/821 `/scratch/stefan/7916156/working/3D/821' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074700.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074700/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074700 none CC(C)C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 13, 23, 13, 13, 13, 13, 13, 6, 13, 6, 1, 6, 1, 1, 1, 1, 1, 1, 13, 23, 23, 23, 23, 23, 23, 23, 13, 13, 13, 13, 13, 6, 1, 13, 13] 23 rigid atoms, others: [35, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37]) total number of confs: 71 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074700 none CC(C)C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 12, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 13, 13, 13, 13, 1, 12, 12, 12, 12, 12, 12, 12, 1, 1, 2, 2, 2, 5, 13, 1, 1] 23 rigid atoms, others: [3, 36, 5, 6, 7, 8, 9, 10, 11, 12, 21, 29, 30, 37] set([0, 1, 2, 4, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35]) total number of confs: 71 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074700 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074700 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074700/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074700 Building REAL250005074701 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074701' /scratch/stefan/7916156/working/building/REAL250005074701 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074701 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074701/0 /scratch/stefan/7916156/working/building/REAL250005074701 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 822) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/822 `/scratch/stefan/7916156/working/3D/822' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074701.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074701.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074701/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074701 none CCC(C)C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [45, 44, 33, 44, 15, 33, 15, 15, 15, 15, 15, 6, 15, 6, 1, 6, 1, 1, 1, 1, 1, 1, 15, 45, 45, 45, 45, 45, 44, 44, 44, 44, 15, 15, 15, 15, 15, 7, 1, 15, 15] 45 rigid atoms, others: [38, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40]) total number of confs: 158 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074701 none CCC(C)C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [28, 20, 7, 20, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 15, 15, 14, 1, 29, 29, 29, 29, 29, 20, 20, 20, 20, 1, 1, 2, 2, 2, 5, 15, 1, 1] 45 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 11, 12, 13, 40, 22, 39] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38]) total number of confs: 159 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074701 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074701 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074701/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074701 Building REAL250005074702 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074702' /scratch/stefan/7916156/working/building/REAL250005074702 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074702 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074702/0 /scratch/stefan/7916156/working/building/REAL250005074702 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 823) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/823 `/scratch/stefan/7916156/working/3D/823' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074702.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074702.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074702/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074702 none COC(C)C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 24, 35, 8, 24, 8, 8, 8, 8, 8, 4, 8, 4, 1, 4, 1, 1, 1, 1, 1, 1, 8, 35, 35, 35, 35, 35, 35, 35, 8, 8, 8, 8, 8, 4, 1, 8, 8] 35 rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 121 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074702 none COC(C)C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [26, 20, 7, 20, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 8, 8, 8, 1, 26, 26, 26, 20, 20, 20, 20, 1, 1, 2, 2, 2, 5, 8, 1, 1] 35 rigid atoms, others: [4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 22, 38, 30, 31] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 105 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074702 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074702 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074702/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074702 Building REAL250005074703 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074703' /scratch/stefan/7916156/working/building/REAL250005074703 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074703 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074703/0 /scratch/stefan/7916156/working/building/REAL250005074703 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 824) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/824 `/scratch/stefan/7916156/working/3D/824' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074703.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074703/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074703 none C=CCCC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [118, 118, 95, 44, 19, 44, 19, 19, 19, 19, 19, 8, 19, 8, 1, 8, 1, 1, 1, 1, 1, 1, 19, 118, 118, 118, 118, 118, 95, 95, 19, 19, 19, 19, 19, 8, 1, 19, 19] 118 rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 470 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074703 none C=CCCC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [95, 58, 34, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 19, 19, 19, 19, 19, 1, 95, 95, 95, 58, 58, 34, 34, 1, 1, 2, 2, 2, 5, 19, 1, 1] 118 rigid atoms, others: [4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 22, 38, 30, 31] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 405 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074703 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074703 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074703/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074703 Building REAL250005074704 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074704' /scratch/stefan/7916156/working/building/REAL250005074704 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074704 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074704/0 /scratch/stefan/7916156/working/building/REAL250005074704 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 825) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/825 `/scratch/stefan/7916156/working/3D/825' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C#N)C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074704.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074704/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074704 none CC(C#N)C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.1', 'N.1', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 16, 23, 23, 12, 16, 12, 12, 12, 12, 12, 5, 12, 5, 1, 5, 1, 1, 1, 1, 1, 1, 12, 23, 23, 23, 23, 12, 12, 12, 12, 12, 6, 1, 12, 12] 23 rigid atoms, others: [33, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35]) total number of confs: 89 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074704 none CC(C#N)C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.1', 'N.1', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [15, 7, 15, 15, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 12, 12, 12, 12, 1, 15, 15, 15, 15, 1, 1, 2, 2, 2, 5, 12, 1, 1] 23 rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 22, 27, 28] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 78 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074704 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074704 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074704/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074704 Building REAL250005074705 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074705' /scratch/stefan/7916156/working/building/REAL250005074705 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074705 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074705/0 /scratch/stefan/7916156/working/building/REAL250005074705 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 826) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/826 `/scratch/stefan/7916156/working/3D/826' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=C(C)C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074705.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074705.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074705/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074705 none CC=C(C)C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 32, 45, 13, 32, 13, 13, 13, 13, 13, 6, 13, 6, 1, 6, 1, 1, 1, 1, 1, 1, 13, 45, 45, 45, 45, 45, 45, 45, 13, 13, 13, 13, 13, 7, 1, 13, 13] 45 rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 143 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074705 none CC=C(C)C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 7, 29, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 13, 13, 13, 13, 1, 29, 29, 29, 29, 29, 29, 29, 1, 1, 2, 2, 2, 5, 13, 1, 1] 45 rigid atoms, others: [4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 22, 38, 30, 31] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 99 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074705 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074705 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074705/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074705 Building REAL250005074706 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074706' /scratch/stefan/7916156/working/building/REAL250005074706 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074706 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074706/0 /scratch/stefan/7916156/working/building/REAL250005074706 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 827) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/827 `/scratch/stefan/7916156/working/3D/827' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074706.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074706/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074706 none CCC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [25, 22, 16, 22, 16, 16, 16, 16, 16, 8, 16, 8, 1, 8, 1, 1, 1, 1, 1, 1, 16, 25, 25, 25, 25, 25, 16, 16, 16, 16, 16, 8, 1, 16, 16] 25 rigid atoms, others: [32, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34]) total number of confs: 83 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074706 none CCC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 16, 16, 16, 16, 16, 1, 12, 12, 12, 12, 12, 1, 1, 2, 2, 2, 5, 16, 1, 1] 25 rigid atoms, others: [33, 2, 4, 5, 6, 7, 8, 9, 10, 11, 34, 20, 26, 27] set([0, 1, 3, 32, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30, 31]) total number of confs: 74 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074706 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074706 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074706/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074706 Building REAL250005074707 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074707' /scratch/stefan/7916156/working/building/REAL250005074707 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074707 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074707/0 /scratch/stefan/7916156/working/building/REAL250005074707 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 828) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/828 `/scratch/stefan/7916156/working/3D/828' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074707.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074707.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074707/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074707 none COCCC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [93, 93, 80, 40, 18, 40, 18, 18, 18, 18, 18, 8, 18, 8, 1, 8, 1, 1, 1, 1, 1, 1, 18, 93, 93, 93, 93, 93, 80, 80, 18, 18, 18, 18, 18, 8, 1, 18, 18] 93 rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 363 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074707 none COCCC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [73, 51, 30, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 18, 18, 18, 18, 18, 1, 74, 73, 73, 51, 51, 30, 30, 1, 1, 2, 2, 2, 5, 18, 1, 1] 93 rigid atoms, others: [4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 22, 38, 30, 31] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 289 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074707 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074707 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074707/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074707 Building REAL250005074708 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074708' /scratch/stefan/7916156/working/building/REAL250005074708 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074708 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074708/0 /scratch/stefan/7916156/working/building/REAL250005074708 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 829) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/829 `/scratch/stefan/7916156/working/3D/829' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074708.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074708.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074708/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074708 none CC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 9, 6, 6, 6, 6, 6, 5, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 9, 9, 9, 6, 6, 6, 6, 6, 5, 1, 6, 6] 9 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: 27 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074708 none CC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 6, 6, 6, 6, 6, 1, 3, 3, 3, 1, 1, 2, 2, 2, 4, 6, 1, 1] 9 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 19, 23, 24, 30, 31] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 25, 26, 27, 28, 29]) total number of confs: 29 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074708 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074708 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074708/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074708 Building REAL250005074709 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074709' /scratch/stefan/7916156/working/building/REAL250005074709 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074709 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074709/0 /scratch/stefan/7916156/working/building/REAL250005074709 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 830) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/830 `/scratch/stefan/7916156/working/3D/830' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2CC2)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005074709.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074709.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074709/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074709 none C[C@@H]1CN(C(=O)C2CC2)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 8, 1, 8, 1, 1, 1, 13, 13, 13, 13, 18, 18, 18, 24, 24, 24, 24, 24, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 13, 13, 18, 24] 24 rigid atoms, others: [5, 7, 8, 9, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 32, 33, 34, 35]) total number of confs: 58 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074709 none C[C@@H]1CN(C(=O)C2CC2)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 4, 13, 13, 1, 1, 1, 1, 5, 5, 5, 10, 10, 10, 10, 10, 2, 2, 2, 1, 1, 13, 13, 13, 13, 13, 1, 1, 5, 10] 24 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 10, 11, 12, 13, 33, 25, 26] set([6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 34, 35]) total number of confs: 58 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.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: REAL250005074709 none C[C@@H]1CN(C(=O)C2CC2)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 15, 15, 24, 24, 10, 6, 10, 6, 1, 6, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 24, 24, 24, 24, 24, 10, 10, 7, 1] 24 rigid atoms, others: [35, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 83 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074709 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074709 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074709/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074709 Building REAL250005074710 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074710' /scratch/stefan/7916156/working/building/REAL250005074710 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074710 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074710/0 /scratch/stefan/7916156/working/building/REAL250005074710 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 831) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/831 `/scratch/stefan/7916156/working/3D/831' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2CCC2)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005074710.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074710/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074710 none C[C@@H]1CN(C(=O)C2CCC2)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 8, 1, 8, 1, 1, 1, 1, 18, 18, 18, 18, 24, 24, 24, 32, 32, 32, 32, 32, 18, 18, 18, 18, 18, 1, 1, 1, 1, 1, 1, 1, 18, 18, 24, 32] 32 rigid atoms, others: [32, 33, 34, 5, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36, 37, 38]) total number of confs: 73 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074710 none C[C@@H]1CN(C(=O)C2CCC2)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 18, 18, 18, 1, 1, 1, 1, 5, 5, 5, 13, 13, 13, 13, 13, 2, 2, 2, 1, 1, 18, 18, 18, 18, 18, 18, 18, 1, 1, 5, 13] 32 rigid atoms, others: [0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 35, 36, 26, 27] set([6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 37, 38]) total number of confs: 77 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.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: REAL250005074710 none C[C@@H]1CN(C(=O)C2CCC2)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 13, 21, 21, 32, 32, 32, 13, 7, 13, 7, 1, 7, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 32, 32, 32, 32, 32, 32, 32, 13, 13, 7, 1] 32 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: 107 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074710 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074710 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074710/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074710 Building REAL250005074711 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074711' /scratch/stefan/7916156/working/building/REAL250005074711 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074711 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074711/0 /scratch/stefan/7916156/working/building/REAL250005074711 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 832) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/832 `/scratch/stefan/7916156/working/3D/832' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C(N)=O)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005074711.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074711.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074711/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074711 none C[C@@H]1CN(C(=O)C(N)=O)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 8, 11, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 4, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 13, 20, 20, 26, 26, 13, 5, 13, 5, 1, 5, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 26, 26, 13, 13, 5, 1] 26 rigid atoms, others: [32, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 81 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074711 none C[C@@H]1CN(C(=O)C(N)=O)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 8, 11, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 4, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 18, 18, 1, 1, 1, 1, 5, 5, 5, 13, 13, 13, 13, 13, 2, 2, 2, 1, 1, 18, 18, 1, 1, 5, 13] 26 rigid atoms, others: [0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 25, 26, 29, 30] set([32, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 31]) total number of confs: 74 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074711 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074711 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074711/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074711 Building REAL250005074712 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074712' /scratch/stefan/7916156/working/building/REAL250005074712 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074712 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074712/0 /scratch/stefan/7916156/working/building/REAL250005074712 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 833) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/833 `/scratch/stefan/7916156/working/3D/833' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C(C)(C)C)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005074712.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074712/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074712 none C[C@@H]1CN(C(=O)C(C)(C)C)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 9, 5, 3, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 5, 3, 1] 9 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: 27 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074712 none C[C@@H]1CN(C(=O)C(C)(C)C)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 4, 4, 5, 5, 5, 5, 5, 2, 2, 2, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 4, 5] 9 rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 11, 12, 13, 14, 26, 27, 37] set([6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40]) total number of confs: 25 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074712 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074712 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074712/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074712 Building REAL250005074713 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074713' /scratch/stefan/7916156/working/building/REAL250005074713 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074713 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074713/0 /scratch/stefan/7916156/working/building/REAL250005074713 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 834) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/834 `/scratch/stefan/7916156/working/3D/834' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2(C)CC2)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005074713.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074713/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074713 none C[C@@H]1CN(C(=O)C2(C)CC2)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 3, 1, 3, 1, 1, 1, 1, 10, 10, 10, 10, 20, 20, 20, 23, 23, 23, 23, 23, 10, 10, 10, 10, 10, 2, 2, 2, 1, 1, 1, 1, 10, 10, 20, 23] 23 rigid atoms, others: [32, 33, 34, 5, 7, 8, 9, 10, 31] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38]) total number of confs: 66 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074713 none C[C@@H]1CN(C(=O)C2(C)CC2)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 10, 10, 10, 1, 1, 1, 1, 5, 5, 5, 10, 10, 10, 9, 10, 2, 2, 2, 1, 1, 10, 10, 10, 10, 10, 10, 10, 1, 1, 5, 10] 23 rigid atoms, others: [0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 35, 36, 26, 27] set([6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 37, 38]) total number of confs: 54 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.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: REAL250005074713 none C[C@@H]1CN(C(=O)C2(C)CC2)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 21, 21, 23, 23, 23, 10, 6, 10, 6, 1, 6, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 23, 23, 23, 23, 23, 23, 23, 10, 10, 6, 1] 23 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: 71 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074713 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074713 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074713/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074713 Building REAL250005074714 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074714' /scratch/stefan/7916156/working/building/REAL250005074714 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074714 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074714/0 /scratch/stefan/7916156/working/building/REAL250005074714 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 835) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/835 `/scratch/stefan/7916156/working/3D/835' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H]1C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074714.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074714/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074714 none C[C@@H]1C[C@H]1C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 6, 26, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 15, 15, 15, 1, 26, 26, 26, 26, 26, 1, 1, 2, 2, 2, 5, 15, 1, 1] 40 rigid atoms, others: [37, 6, 8, 9, 10, 11, 12, 13, 14, 15, 24, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 95 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074714 none C[C@@H]1C[C@H]1C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 8, 8, 26, 26, 26, 26, 26, 26, 26, 36, 36, 36, 40, 40, 40, 40, 40, 26, 2, 2, 2, 1, 1, 26, 26, 26, 26, 26, 36, 40, 26, 26] 40 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 96 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.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: REAL250005074714 none C[C@@H]1C[C@H]1C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 32, 40, 15, 32, 15, 15, 15, 15, 15, 6, 15, 6, 1, 6, 1, 1, 1, 1, 1, 1, 15, 40, 40, 40, 40, 40, 15, 15, 15, 15, 15, 6, 1, 15, 15] 40 rigid atoms, others: [36, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 127 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074714 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074714 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074714/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074714 Building REAL250005074715 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074715' /scratch/stefan/7916156/working/building/REAL250005074715 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074715 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074715/0 /scratch/stefan/7916156/working/building/REAL250005074715 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 836) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/836 `/scratch/stefan/7916156/working/3D/836' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(F)C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074715.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074715/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074715 none CCC(F)C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 36, 59, 15, 36, 15, 15, 15, 15, 15, 6, 15, 6, 1, 6, 1, 1, 1, 1, 1, 1, 15, 59, 59, 59, 59, 59, 59, 15, 15, 15, 15, 15, 6, 1, 15, 15] 59 rigid atoms, others: [35, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37]) total number of confs: 207 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074715 none CCC(F)C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [38, 29, 6, 29, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 15, 15, 15, 1, 42, 42, 42, 42, 42, 29, 1, 1, 2, 2, 2, 5, 15, 1, 1] 59 rigid atoms, others: [4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 22, 36, 29, 30] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35]) total number of confs: 230 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074715 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074715 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074715/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074715 Building REAL250005074716 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074716' /scratch/stefan/7916156/working/building/REAL250005074716 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074716 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074716/0 /scratch/stefan/7916156/working/building/REAL250005074716 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 837) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/837 `/scratch/stefan/7916156/working/3D/837' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)CCCF)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005074716.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074716/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074716 none C[C@@H]1CN(C(=O)CCCF)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 15, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 106 conformations in input total number of sets (complete confs): 106 using faster count positions algorithm for large data unique positions, atoms: [14, 14, 14, 14, 14, 14, 35, 35, 89, 103, 106, 14, 7, 14, 7, 1, 7, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 89, 89, 106, 106, 106, 106, 14, 14, 7, 1] 106 rigid atoms, others: [37, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 433 number of broken/clashed sets: 14 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074716 none C[C@@H]1CN(C(=O)CCCF)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 15, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 106 conformations in input total number of sets (complete confs): 106 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 29, 39, 79, 1, 1, 1, 1, 5, 5, 5, 14, 14, 14, 14, 14, 2, 2, 2, 1, 1, 29, 29, 48, 48, 71, 75, 1, 1, 5, 14] 106 rigid atoms, others: [0, 1, 2, 3, 4, 5, 11, 12, 34, 14, 13, 35, 26, 27] set([6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 36, 37]) total number of confs: 406 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074716 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074716 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074716/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074716 Building REAL250005074717 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074717' /scratch/stefan/7916156/working/building/REAL250005074717 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074717 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074717/0 /scratch/stefan/7916156/working/building/REAL250005074717 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 838) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/838 `/scratch/stefan/7916156/working/3D/838' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@@H]1C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074717.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074717/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074717 none C[C@H]1C[C@@H]1C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 7, 20, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 13, 13, 13, 13, 1, 20, 20, 20, 20, 20, 1, 1, 2, 2, 2, 5, 13, 1, 1] 33 rigid atoms, others: [37, 6, 8, 9, 10, 11, 12, 13, 14, 15, 24, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 80 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074717 none C[C@H]1C[C@@H]1C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 7, 20, 20, 20, 20, 20, 20, 20, 30, 30, 30, 33, 33, 33, 33, 33, 20, 2, 2, 2, 1, 1, 20, 20, 20, 20, 20, 30, 33, 20, 20] 33 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 84 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.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: REAL250005074717 none C[C@H]1C[C@@H]1C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 30, 33, 13, 30, 13, 13, 13, 13, 13, 7, 13, 7, 1, 7, 1, 1, 1, 1, 1, 1, 13, 33, 33, 33, 33, 33, 13, 13, 13, 13, 13, 7, 1, 13, 13] 33 rigid atoms, others: [36, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 95 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074717 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074717 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074717/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074717 Building REAL250005074718 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074718' /scratch/stefan/7916156/working/building/REAL250005074718 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074718 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074718/0 /scratch/stefan/7916156/working/building/REAL250005074718 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 839) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/839 `/scratch/stefan/7916156/working/3D/839' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)CO)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005074718.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074718/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074718 none C[C@@H]1CN(C(=O)CO)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 12, 12, 12, 16, 16, 18, 12, 6, 12, 6, 1, 6, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 18, 18, 54, 12, 12, 6, 1] 54 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: 113 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074718 none C[C@@H]1CN(C(=O)CO)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 4, 11, 1, 1, 1, 1, 5, 5, 5, 12, 12, 12, 12, 12, 2, 2, 2, 1, 1, 11, 11, 33, 1, 1, 5, 12] 54 rigid atoms, others: [0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 24, 25, 29, 30] set([32, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 31]) total number of confs: 95 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074718 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074718 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074718/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074718 Building REAL250005074719 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074719' /scratch/stefan/7916156/working/building/REAL250005074719 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074719 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074719/0 /scratch/stefan/7916156/working/building/REAL250005074719 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 840) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/840 `/scratch/stefan/7916156/working/3D/840' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2CCO2)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005074719.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074719/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074719 none C[C@@H]1CN(C(=O)C2CCO2)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 8, 1, 8, 1, 1, 1, 1, 23, 23, 23, 23, 31, 31, 31, 32, 32, 32, 32, 32, 23, 23, 23, 23, 23, 1, 1, 1, 1, 1, 23, 23, 31, 32] 32 rigid atoms, others: [32, 5, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35, 36]) total number of confs: 72 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074719 none C[C@@H]1CN(C(=O)C2CCO2)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 23, 23, 23, 1, 1, 1, 1, 5, 5, 5, 12, 12, 12, 12, 12, 2, 2, 2, 1, 1, 23, 23, 23, 23, 23, 1, 1, 5, 12] 32 rigid atoms, others: [0, 1, 2, 3, 4, 5, 33, 11, 12, 34, 14, 13, 26, 27] set([6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 35, 36]) total number of confs: 84 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.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: REAL250005074719 none C[C@@H]1CN(C(=O)C2CCO2)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 12, 12, 25, 25, 32, 32, 32, 12, 5, 12, 5, 1, 5, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 32, 32, 32, 32, 32, 12, 12, 5, 1] 32 rigid atoms, others: [36, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 97 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074719 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074719 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074719/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074719 Building REAL250005074720 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074720' /scratch/stefan/7916156/working/building/REAL250005074720 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074720 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074720/0 /scratch/stefan/7916156/working/building/REAL250005074720 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 841) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/841 `/scratch/stefan/7916156/working/3D/841' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2COC2)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005074720.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074720.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074720/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074720 none C[C@@H]1CN(C(=O)C2COC2)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 7, 1, 7, 1, 1, 1, 1, 19, 19, 19, 19, 28, 28, 28, 32, 32, 32, 32, 32, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 19, 19, 28, 32] 32 rigid atoms, others: [32, 5, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35, 36]) total number of confs: 74 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074720 none C[C@@H]1CN(C(=O)C2COC2)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 19, 19, 19, 1, 1, 1, 1, 5, 5, 5, 15, 15, 15, 15, 15, 2, 2, 2, 1, 1, 19, 19, 19, 19, 19, 1, 1, 5, 15] 32 rigid atoms, others: [0, 1, 2, 3, 4, 5, 33, 11, 12, 34, 14, 13, 26, 27] set([6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 35, 36]) total number of confs: 81 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.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: REAL250005074720 none C[C@@H]1CN(C(=O)C2COC2)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 15, 15, 24, 24, 32, 32, 32, 15, 8, 15, 8, 1, 8, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 32, 32, 32, 32, 32, 15, 15, 8, 1] 32 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: 103 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074720 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074720 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074720/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074720 Building REAL250005074721 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074721' /scratch/stefan/7916156/working/building/REAL250005074721 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074721 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074721/0 /scratch/stefan/7916156/working/building/REAL250005074721 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 842) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/842 `/scratch/stefan/7916156/working/3D/842' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C=CCO)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005074721.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074721/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074721 none C[C@@H]1CN(C(=O)C=CCO)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 5, 12, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 222 conformations in input total number of sets (complete confs): 222 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 23, 23, 23, 23, 45, 45, 71, 71, 74, 23, 8, 23, 8, 1, 8, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 71, 71, 74, 74, 222, 23, 23, 9, 1] 222 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: 449 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074721 none C[C@@H]1CN(C(=O)C=CCO)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 5, 12, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 222 conformations in input total number of sets (complete confs): 222 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 28, 28, 61, 1, 1, 1, 1, 5, 5, 5, 23, 23, 23, 23, 23, 2, 2, 2, 1, 1, 28, 28, 61, 61, 183, 1, 1, 5, 23] 222 rigid atoms, others: [0, 1, 2, 3, 4, 5, 33, 11, 12, 34, 14, 13, 26, 27] set([6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 35, 36]) total number of confs: 443 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074721 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074721 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074721/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074721 Building REAL250005074722 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074722' /scratch/stefan/7916156/working/building/REAL250005074722 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074722 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074722/0 /scratch/stefan/7916156/working/building/REAL250005074722 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 843) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/843 `/scratch/stefan/7916156/working/3D/843' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC=CC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074722.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074722/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074722 none CCC=CC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [80, 69, 69, 49, 22, 49, 22, 22, 22, 22, 22, 10, 22, 10, 1, 10, 1, 1, 1, 1, 1, 1, 22, 80, 80, 80, 80, 80, 69, 69, 22, 22, 22, 22, 22, 11, 1, 22, 22] 80 rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 273 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074722 none CCC=CC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [51, 30, 30, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 22, 22, 22, 22, 22, 1, 51, 51, 51, 51, 51, 29, 30, 1, 1, 2, 2, 2, 5, 22, 1, 1] 80 rigid atoms, others: [4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 22, 38, 30, 31] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 231 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074722 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074722 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074722/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074722 Building REAL250005074723 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074723' /scratch/stefan/7916156/working/building/REAL250005074723 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074723 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074723/0 /scratch/stefan/7916156/working/building/REAL250005074723 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 844) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/844 `/scratch/stefan/7916156/working/3D/844' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074723.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074723/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074723 none C#CCCC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [75, 75, 71, 33, 12, 33, 12, 12, 12, 12, 12, 6, 12, 6, 1, 6, 1, 1, 1, 1, 1, 1, 12, 75, 75, 75, 71, 71, 12, 12, 12, 12, 12, 6, 1, 12, 12] 75 rigid atoms, others: [34, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36]) total number of confs: 282 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074723 none C#CCCC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [53, 52, 34, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 12, 12, 12, 12, 1, 53, 52, 52, 34, 34, 1, 1, 2, 2, 2, 5, 12, 1, 1] 75 rigid atoms, others: [35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 22, 36, 28, 29] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34]) total number of confs: 246 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074723 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074723 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074723/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074723 Building REAL250005074724 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074724' /scratch/stefan/7916156/working/building/REAL250005074724 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074724 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074724/0 /scratch/stefan/7916156/working/building/REAL250005074724 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 845) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/845 `/scratch/stefan/7916156/working/3D/845' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(O)C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074724.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074724.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074724/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074724 none C=CC(O)C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 171 conformations in input total number of sets (complete confs): 171 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 37, 57, 15, 37, 15, 15, 15, 15, 15, 7, 15, 7, 1, 7, 1, 1, 1, 1, 1, 1, 15, 57, 57, 57, 57, 171, 15, 15, 15, 15, 15, 7, 1, 15, 15] 171 rigid atoms, others: [34, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36]) total number of confs: 366 number of broken/clashed sets: 19 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074724 none C=CC(O)C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 171 conformations in input total number of sets (complete confs): 171 using faster count positions algorithm for large data unique positions, atoms: [40, 26, 7, 26, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 15, 15, 15, 1, 40, 40, 40, 26, 78, 1, 1, 2, 2, 2, 5, 15, 1, 1] 171 rigid atoms, others: [35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 22, 36, 28, 29] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34]) total number of confs: 251 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074724 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074724 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074724/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074724 Building REAL250005074725 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074725' /scratch/stefan/7916156/working/building/REAL250005074725 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074725 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074725/0 /scratch/stefan/7916156/working/building/REAL250005074725 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 846) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/846 `/scratch/stefan/7916156/working/3D/846' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074725.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074725/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074725 none CC(O)C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [20, 18, 20, 10, 18, 10, 10, 10, 10, 10, 5, 10, 5, 1, 5, 1, 1, 1, 1, 1, 1, 10, 20, 20, 20, 20, 60, 10, 10, 10, 10, 10, 6, 1, 10, 10] 60 rigid atoms, others: [33, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35]) total number of confs: 123 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074725 none CC(O)C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [16, 7, 16, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 10, 10, 10, 10, 1, 16, 16, 16, 16, 48, 1, 1, 2, 2, 2, 5, 10, 1, 1] 60 rigid atoms, others: [34, 3, 5, 6, 7, 8, 9, 10, 11, 12, 35, 21, 27, 28] set([0, 1, 2, 4, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 127 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074725 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074725 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074725/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074725 Building REAL250005074726 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074726' /scratch/stefan/7916156/working/building/REAL250005074726 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074726 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074726/0 /scratch/stefan/7916156/working/building/REAL250005074726 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 847) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/847 `/scratch/stefan/7916156/working/3D/847' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074726.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074726.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074726/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074726 none CC(=O)C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [24, 17, 24, 11, 17, 11, 11, 11, 11, 11, 5, 11, 5, 1, 5, 1, 1, 1, 1, 1, 1, 11, 24, 24, 24, 11, 11, 11, 11, 11, 6, 1, 11, 11] 24 rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33]) total number of confs: 77 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074726 none CC(=O)C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 16, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 11, 11, 11, 11, 11, 1, 15, 15, 15, 1, 1, 2, 2, 2, 5, 11, 1, 1] 24 rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 10, 11, 12, 21, 25, 26] set([0, 1, 2, 4, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 27, 28, 29, 30, 31]) total number of confs: 64 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074726 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074726 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074726/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074726 Building REAL250005074727 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074727' /scratch/stefan/7916156/working/building/REAL250005074727 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074727 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074727/0 /scratch/stefan/7916156/working/building/REAL250005074727 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 848) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/848 `/scratch/stefan/7916156/working/3D/848' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2(F)CC2)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005074727.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074727/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074727 none C[C@@H]1CN(C(=O)C2(F)CC2)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 9, 1, 9, 1, 1, 1, 1, 23, 23, 23, 23, 30, 30, 30, 31, 31, 31, 31, 31, 23, 23, 23, 23, 23, 1, 1, 1, 1, 23, 23, 30, 31] 31 rigid atoms, others: [5, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35]) total number of confs: 67 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074727 none C[C@@H]1CN(C(=O)C2(F)CC2)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 23, 23, 23, 1, 1, 1, 1, 5, 5, 5, 11, 11, 11, 11, 11, 2, 2, 2, 1, 1, 23, 23, 23, 23, 1, 1, 5, 11] 31 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 11, 12, 13, 14, 33, 26, 27] set([6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 34, 35]) total number of confs: 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.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: REAL250005074727 none C[C@@H]1CN(C(=O)C2(F)CC2)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 25, 25, 31, 31, 31, 11, 5, 11, 5, 1, 5, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 31, 31, 31, 31, 11, 11, 5, 1] 31 rigid atoms, others: [35, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 91 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074727 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074727 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074727/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074727 Building REAL250005074728 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074728' /scratch/stefan/7916156/working/building/REAL250005074728 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074728 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074728/0 /scratch/stefan/7916156/working/building/REAL250005074728 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 849) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/849 `/scratch/stefan/7916156/working/3D/849' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=C(F)C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074728.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074728/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074728 none CC=C(F)C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 25, 30, 11, 25, 11, 11, 11, 11, 11, 6, 11, 6, 1, 6, 1, 1, 1, 1, 1, 1, 11, 30, 30, 30, 30, 11, 11, 11, 11, 11, 6, 1, 11, 11] 30 rigid atoms, others: [33, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35]) total number of confs: 91 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074728 none CC=C(F)C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [21, 20, 6, 21, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 11, 11, 11, 11, 11, 1, 20, 21, 21, 20, 1, 1, 2, 2, 2, 5, 11, 1, 1] 30 rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 22, 27, 28] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 81 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074728 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074728 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074728/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074728 Building REAL250005074729 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074729' /scratch/stefan/7916156/working/building/REAL250005074729 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074729 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074729/0 /scratch/stefan/7916156/working/building/REAL250005074729 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 850) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/850 `/scratch/stefan/7916156/working/3D/850' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CO)C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074729.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074729/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074729 none CC(CO)C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [27, 21, 27, 27, 8, 21, 8, 8, 8, 8, 8, 4, 8, 4, 1, 4, 1, 1, 1, 1, 1, 1, 8, 27, 27, 27, 27, 27, 27, 81, 8, 8, 8, 8, 8, 4, 1, 8, 8] 81 rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 174 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074729 none CC(CO)C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 13, 24, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 8, 8, 8, 1, 13, 13, 13, 13, 24, 24, 72, 1, 1, 2, 2, 2, 5, 8, 1, 1] 81 rigid atoms, others: [4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 22, 38, 30, 31] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 192 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074729 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074729 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074729/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074729 Building REAL250005074730 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074730' /scratch/stefan/7916156/working/building/REAL250005074730 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074730 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074730/0 /scratch/stefan/7916156/working/building/REAL250005074730 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 851) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/851 `/scratch/stefan/7916156/working/3D/851' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2(O)CC2)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005074730.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074730/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074730 none C[C@@H]1CN(C(=O)C2(O)CC2)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 21, 8, 1, 8, 1, 1, 1, 1, 21, 21, 21, 21, 27, 27, 27, 30, 30, 30, 30, 30, 21, 21, 21, 21, 21, 6, 1, 1, 1, 1, 21, 21, 27, 30] 90 rigid atoms, others: [32, 5, 7, 8, 9, 10, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36]) total number of confs: 70 number of broken/clashed sets: 21 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074730 none C[C@@H]1CN(C(=O)C2(O)CC2)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 6, 6, 21, 21, 21, 1, 1, 1, 1, 5, 5, 5, 11, 11, 11, 11, 11, 2, 2, 2, 1, 1, 63, 21, 21, 21, 21, 1, 1, 5, 11] 90 rigid atoms, others: [0, 1, 2, 3, 4, 5, 33, 11, 12, 34, 14, 13, 26, 27] set([6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 35, 36]) total number of confs: 141 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.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: REAL250005074730 none C[C@@H]1CN(C(=O)C2(O)CC2)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 11, 11, 11, 20, 20, 30, 30, 30, 11, 6, 11, 6, 1, 6, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 90, 30, 30, 30, 30, 11, 11, 7, 1] 90 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: 189 number of broken/clashed sets: 21 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074730 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074730 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074730/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074730 Building REAL250005074731 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074731' /scratch/stefan/7916156/working/building/REAL250005074731 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074731 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074731/0 /scratch/stefan/7916156/working/building/REAL250005074731 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 852) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/852 `/scratch/stefan/7916156/working/3D/852' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CCC2)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005074731.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074731.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074731/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074731 none C[C@@H]1CN(C(=O)C2=CCC2)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 8, 1, 8, 1, 1, 1, 1, 15, 15, 15, 15, 24, 24, 24, 26, 26, 26, 26, 26, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 15, 15, 24, 26] 26 rigid atoms, others: [32, 5, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35, 36]) total number of confs: 63 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074731 none C[C@@H]1CN(C(=O)C2=CCC2)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 15, 15, 15, 1, 1, 1, 1, 5, 5, 5, 14, 14, 14, 14, 14, 2, 2, 2, 1, 1, 15, 15, 15, 15, 15, 1, 1, 5, 14] 26 rigid atoms, others: [0, 1, 2, 3, 4, 5, 33, 11, 12, 34, 14, 13, 26, 27] set([6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 35, 36]) total number of confs: 58 number of broken/clashed sets: 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.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: REAL250005074731 none C[C@@H]1CN(C(=O)C2=CCC2)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 14, 26, 26, 26, 26, 26, 14, 7, 14, 7, 1, 7, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 26, 26, 26, 26, 26, 14, 14, 7, 1] 26 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: 73 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074731 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074731 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074731/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074731 Building REAL250005074732 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074732' /scratch/stefan/7916156/working/building/REAL250005074732 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074732 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074732/0 /scratch/stefan/7916156/working/building/REAL250005074732 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 853) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/853 `/scratch/stefan/7916156/working/3D/853' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CF)C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074732.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074732/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074732 none CC(CF)C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [33, 24, 33, 34, 13, 24, 13, 13, 13, 13, 13, 5, 13, 5, 1, 5, 1, 1, 1, 1, 1, 1, 13, 33, 33, 33, 33, 34, 34, 13, 13, 13, 13, 13, 5, 1, 13, 13] 34 rigid atoms, others: [35, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37]) total number of confs: 124 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074732 none CC(CF)C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 14, 27, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 13, 13, 13, 13, 1, 14, 14, 14, 14, 27, 27, 1, 1, 2, 2, 2, 5, 13, 1, 1] 34 rigid atoms, others: [4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 22, 36, 29, 30] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35]) total number of confs: 131 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074732 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074732 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074732/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074732 Building REAL250005074733 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074733' /scratch/stefan/7916156/working/building/REAL250005074733 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074733 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074733/0 /scratch/stefan/7916156/working/building/REAL250005074733 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 854) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/854 `/scratch/stefan/7916156/working/3D/854' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074733.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074733/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074733 none CC=CC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 20, 11, 20, 11, 11, 11, 11, 11, 6, 11, 6, 1, 6, 1, 1, 1, 1, 1, 1, 11, 23, 23, 23, 23, 23, 11, 11, 11, 11, 11, 6, 1, 11, 11] 23 rigid atoms, others: [33, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35]) total number of confs: 69 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074733 none CC=CC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [17, 16, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 11, 11, 11, 11, 11, 1, 17, 17, 17, 16, 16, 1, 1, 2, 2, 2, 5, 11, 1, 1] 23 rigid atoms, others: [34, 3, 5, 6, 7, 8, 9, 10, 11, 12, 35, 21, 27, 28] set([0, 1, 2, 4, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 69 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074733 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074733 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074733/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074733 Building REAL250005074734 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074734' /scratch/stefan/7916156/working/building/REAL250005074734 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074734 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074734/0 /scratch/stefan/7916156/working/building/REAL250005074734 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 855) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/855 `/scratch/stefan/7916156/working/3D/855' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C=CCF)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005074734.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074734/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074734 none C[C@@H]1CN(C(=O)C=CCF)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'F', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 5, 15, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 13, 13, 13, 29, 29, 56, 56, 56, 13, 6, 13, 6, 1, 6, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 56, 56, 56, 56, 13, 13, 7, 1] 56 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: 169 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074734 none C[C@@H]1CN(C(=O)C=CCF)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'F', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 5, 15, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 25, 25, 47, 1, 1, 1, 1, 5, 5, 5, 13, 13, 13, 13, 13, 2, 2, 2, 1, 1, 25, 25, 47, 47, 1, 1, 5, 13] 56 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 11, 12, 13, 14, 33, 26, 27] set([6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 34, 35]) total number of confs: 191 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074734 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074734 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074734/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074734 Building REAL250005074735 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074735' /scratch/stefan/7916156/working/building/REAL250005074735 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types Protomer extracton resulted in 0 protomers Marking REAL250005074735 as failed and skipping /scratch/stefan/7916156/working /scratch/stefan/7916156 `/scratch/stefan/7916156/working/building/REAL250005074735' -> `/scratch/stefan/7916156/failed/REAL250005074735' Building REAL250005074736 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074736' /scratch/stefan/7916156/working/building/REAL250005074736 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074736 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074736/0 /scratch/stefan/7916156/working/building/REAL250005074736 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 856) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/856 `/scratch/stefan/7916156/working/3D/856' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074736.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074736/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074736 none C[C@H](O)C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [25, 18, 25, 25, 9, 18, 9, 9, 9, 9, 9, 6, 9, 6, 1, 6, 1, 1, 1, 1, 1, 1, 9, 25, 25, 25, 75, 9, 9, 9, 9, 9, 6, 1, 9, 9] 75 rigid atoms, others: [33, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35]) total number of confs: 158 number of broken/clashed sets: 18 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074736 none C[C@H](O)C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [16, 6, 16, 16, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 9, 9, 9, 9, 1, 16, 16, 16, 48, 1, 1, 2, 2, 2, 5, 9, 1, 1] 75 rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 22, 27, 28] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 125 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074736 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074736 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074736/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074736 Building REAL250005074737 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074737' /scratch/stefan/7916156/working/building/REAL250005074737 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074737 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074737/0 /scratch/stefan/7916156/working/building/REAL250005074737 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 857) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/857 `/scratch/stefan/7916156/working/3D/857' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CON=CC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074737.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074737.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074737/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074737 none CON=CC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 8, 1, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 30, 11, 30, 11, 11, 11, 11, 11, 6, 11, 7, 1, 7, 1, 1, 1, 1, 1, 1, 11, 47, 47, 47, 47, 11, 11, 11, 11, 11, 7, 1, 11, 11] 47 rigid atoms, others: [33, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35]) total number of confs: 140 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074737 none CON=CC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 8, 1, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [37, 32, 32, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 11, 11, 11, 11, 11, 1, 37, 37, 37, 32, 1, 1, 2, 2, 2, 5, 11, 1, 1] 47 rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 22, 27, 28] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 112 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074737 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074737 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074737/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074737 Building REAL250005074738 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074738' /scratch/stefan/7916156/working/building/REAL250005074738 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074738 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074738/0 /scratch/stefan/7916156/working/building/REAL250005074738 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 858) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/858 `/scratch/stefan/7916156/working/3D/858' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H]1C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074738.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074738/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074738 none C[C@@H]1C[C@H]1C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 6, 26, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 15, 15, 15, 1, 26, 26, 26, 26, 26, 1, 1, 2, 2, 2, 5, 15, 1, 1] 40 rigid atoms, others: [37, 6, 8, 9, 10, 11, 12, 13, 14, 15, 24, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 95 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074738 none C[C@@H]1C[C@H]1C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 8, 8, 26, 26, 26, 26, 26, 26, 26, 36, 36, 36, 40, 40, 40, 40, 40, 26, 2, 2, 2, 1, 1, 26, 26, 26, 26, 26, 36, 40, 26, 26] 40 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 96 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.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: REAL250005074738 none C[C@@H]1C[C@H]1C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 32, 40, 15, 32, 15, 15, 15, 15, 15, 6, 15, 6, 1, 6, 1, 1, 1, 1, 1, 1, 15, 40, 40, 40, 40, 40, 15, 15, 15, 15, 15, 6, 1, 15, 15] 40 rigid atoms, others: [36, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 127 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074738 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074738 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074738/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074738 Building REAL250005074739 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074739' /scratch/stefan/7916156/working/building/REAL250005074739 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074739 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074739/0 /scratch/stefan/7916156/working/building/REAL250005074739 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 859) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/859 `/scratch/stefan/7916156/working/3D/859' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C(C)(C)O)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005074739.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074739/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074739 none C[C@@H]1CN(C(=O)C(C)(C)O)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 10, 10, 10, 10, 20, 20, 24, 24, 24, 10, 6, 10, 6, 1, 6, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 24, 24, 24, 24, 24, 24, 72, 10, 10, 6, 1] 72 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: 151 number of broken/clashed sets: 28 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074739 none C[C@@H]1CN(C(=O)C(C)(C)O)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 14, 14, 14, 1, 1, 1, 1, 5, 5, 5, 10, 10, 10, 10, 10, 2, 2, 2, 1, 1, 14, 14, 14, 14, 14, 14, 42, 1, 1, 5, 10] 72 rigid atoms, others: [0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 35, 36, 26, 27] set([6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 37, 38]) total number of confs: 121 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074739 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074739 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074739/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074739 Building REAL250005074740 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074740' /scratch/stefan/7916156/working/building/REAL250005074740 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074740 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074740/0 /scratch/stefan/7916156/working/building/REAL250005074740 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 860) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/860 `/scratch/stefan/7916156/working/3D/860' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)CC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074740.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074740/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074740 none C=C(C)CC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [83, 83, 83, 45, 19, 45, 19, 19, 19, 19, 19, 7, 19, 7, 1, 7, 1, 1, 1, 1, 1, 1, 19, 83, 83, 83, 83, 83, 83, 83, 19, 19, 19, 19, 19, 7, 1, 19, 19] 83 rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 308 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074740 none C=C(C)CC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [55, 37, 55, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 19, 19, 19, 19, 19, 1, 55, 55, 55, 55, 55, 38, 38, 1, 1, 2, 2, 2, 5, 19, 1, 1] 83 rigid atoms, others: [4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 22, 38, 30, 31] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 224 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074740 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074740 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074740/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074740 Building REAL250005074741 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074741' /scratch/stefan/7916156/working/building/REAL250005074741 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074741 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074741/0 /scratch/stefan/7916156/working/building/REAL250005074741 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 861) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/861 `/scratch/stefan/7916156/working/3D/861' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074741.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074741/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074741 none C=CCC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [62, 62, 40, 18, 40, 18, 18, 18, 18, 18, 8, 18, 8, 1, 8, 1, 1, 1, 1, 1, 1, 18, 62, 62, 62, 62, 62, 18, 18, 18, 18, 18, 8, 1, 18, 18] 62 rigid atoms, others: [33, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35]) total number of confs: 222 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074741 none C=CCC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [44, 24, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 18, 18, 18, 18, 18, 1, 44, 44, 44, 24, 24, 1, 1, 2, 2, 2, 5, 18, 1, 1] 62 rigid atoms, others: [34, 3, 5, 6, 7, 8, 9, 10, 11, 12, 35, 21, 27, 28] set([0, 1, 2, 4, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 186 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074741 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074741 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074741/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074741 Building REAL250005074742 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074742' /scratch/stefan/7916156/working/building/REAL250005074742 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005074742 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074742/0 /scratch/stefan/7916156/working/building/REAL250005074742 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 862) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/862 `/scratch/stefan/7916156/working/3D/862' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C[NH+](C)C)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005074742.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074742/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074742 none C[C@@H]1CN(C(=O)C[NH+](C)C)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 12, 12, 15, 15, 16, 16, 16, 16, 12, 6, 12, 6, 1, 6, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 16, 16, 16, 16, 16, 16, 16, 16, 12, 12, 7, 1] 16 rigid atoms, others: [40, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 51 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074742 none C[C@@H]1CN(C(=O)C[NH+](C)C)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 11, 11, 11, 11, 1, 1, 1, 1, 5, 5, 5, 12, 12, 12, 12, 12, 2, 2, 2, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 5, 12] 16 rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 12, 13, 14, 15, 27, 28, 37] set([6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40]) total number of confs: 63 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074742 /scratch/stefan/7916156/working /scratch/stefan/7916156 mkdir: created directory `1' /scratch/stefan/7916156/working/building/REAL250005074742/1 /scratch/stefan/7916156/working/building/REAL250005074742 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 1 (index: 863) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/863 `/scratch/stefan/7916156/working/3D/863' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)CN(C)C)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005074742.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005074742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074742/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074742 none C[C@@H]1CN(C(=O)CN(C)C)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 11, 11, 11, 24, 24, 55, 56, 56, 11, 6, 11, 6, 1, 6, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 55, 55, 56, 56, 56, 56, 56, 56, 11, 11, 7, 1] 56 rigid atoms, others: [39, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 215 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074742 none C[C@@H]1CN(C(=O)CN(C)C)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 31, 46, 46, 1, 1, 1, 1, 4, 4, 4, 11, 11, 11, 11, 11, 2, 2, 2, 1, 1, 31, 31, 46, 46, 46, 46, 46, 46, 1, 1, 4, 11] 56 rigid atoms, others: [0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 36, 26, 27, 37] set([6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074742 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074742 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 1: /scratch/stefan/7916156/working/building/REAL250005074742/1.* 0: /scratch/stefan/7916156/working/building/REAL250005074742/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074742 Building REAL250005074743 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074743' /scratch/stefan/7916156/working/building/REAL250005074743 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074743 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074743/0 /scratch/stefan/7916156/working/building/REAL250005074743 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 864) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/864 `/scratch/stefan/7916156/working/3D/864' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)CC#N)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005074743.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074743.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074743/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074743 none C[C@@H]1CN(C(=O)CC#N)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.1', 'N.1', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 1, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 14, 23, 23, 40, 40, 14, 6, 14, 6, 1, 6, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 40, 40, 14, 14, 7, 1] 40 rigid atoms, others: [32, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 152 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074743 none C[C@@H]1CN(C(=O)CC#N)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.1', 'N.1', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 1, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 25, 25, 1, 1, 1, 1, 5, 5, 5, 14, 14, 14, 14, 14, 2, 2, 2, 1, 1, 25, 25, 1, 1, 5, 14] 40 rigid atoms, others: [0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 25, 26, 29, 30] set([32, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 31]) total number of confs: 113 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074743 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074743 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074743/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074743 Building REAL250005074744 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074744' /scratch/stefan/7916156/working/building/REAL250005074744 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074744 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074744/0 /scratch/stefan/7916156/working/building/REAL250005074744 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 865) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/865 `/scratch/stefan/7916156/working/3D/865' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2CC2F)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005074744.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074744.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074744/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074744 none C[C@@H]1CN(C(=O)C2CC2F)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 15, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 8, 1, 8, 1, 1, 1, 1, 22, 22, 22, 22, 36, 36, 36, 38, 38, 38, 38, 38, 22, 22, 22, 22, 22, 1, 1, 1, 1, 22, 22, 36, 38] 38 rigid atoms, others: [5, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35]) total number of confs: 93 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074744 none C[C@@H]1CN(C(=O)C2CC2F)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 15, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 22, 22, 22, 1, 1, 1, 1, 5, 5, 5, 16, 16, 16, 16, 16, 2, 2, 2, 1, 1, 22, 22, 22, 22, 1, 1, 5, 16] 38 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 11, 12, 13, 14, 33, 26, 27] set([6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 34, 35]) total number of confs: 86 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.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: REAL250005074744 none C[C@@H]1CN(C(=O)C2CC2F)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 15, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 16, 28, 28, 38, 38, 38, 16, 8, 16, 8, 1, 8, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 38, 38, 38, 38, 16, 16, 8, 1] 38 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: 115 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074744 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074744 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074744/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074744 Building REAL250005074745 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074745' /scratch/stefan/7916156/working/building/REAL250005074745 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074745 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074745/0 /scratch/stefan/7916156/working/building/REAL250005074745 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 866) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/866 `/scratch/stefan/7916156/working/3D/866' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)CCF)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005074745.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074745/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074745 none C[C@@H]1CN(C(=O)CCF)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 15, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 12, 12, 12, 28, 28, 51, 51, 12, 5, 12, 5, 1, 5, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 51, 51, 51, 51, 12, 12, 5, 1] 51 rigid atoms, others: [34, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 188 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074745 none C[C@@H]1CN(C(=O)CCF)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 15, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 18, 31, 1, 1, 1, 1, 5, 5, 5, 12, 12, 12, 12, 12, 2, 2, 2, 1, 1, 18, 18, 31, 31, 1, 1, 5, 12] 51 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 10, 11, 12, 13, 25, 26, 31] set([33, 34, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30]) total number of confs: 155 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074745 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074745 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074745/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074745 Building REAL250005074746 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074746' /scratch/stefan/7916156/working/building/REAL250005074746 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074746 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074746/0 /scratch/stefan/7916156/working/building/REAL250005074746 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 867) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/867 `/scratch/stefan/7916156/working/3D/867' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](C)C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074746.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074746/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074746 none CO[C@H](C)C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 20, 28, 28, 9, 20, 9, 9, 9, 9, 9, 4, 9, 4, 1, 4, 1, 1, 1, 1, 1, 1, 9, 28, 28, 28, 28, 28, 28, 9, 9, 9, 9, 9, 5, 1, 9, 9] 28 rigid atoms, others: [36, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 100 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074746 none CO[C@H](C)C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [24, 19, 7, 19, 19, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 9, 9, 9, 9, 1, 24, 24, 24, 19, 19, 19, 1, 1, 2, 2, 2, 5, 9, 1, 1] 28 rigid atoms, others: [5, 38, 7, 8, 9, 10, 11, 12, 13, 14, 23, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 100 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074746 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074746 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074746/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074746 Building REAL250005074747 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074747' /scratch/stefan/7916156/working/building/REAL250005074747 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074747 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074747/0 /scratch/stefan/7916156/working/building/REAL250005074747 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 868) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/868 `/scratch/stefan/7916156/working/3D/868' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074747.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074747/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074747 none C[C@@H](O)C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [19, 17, 19, 19, 9, 17, 9, 9, 9, 9, 9, 4, 9, 4, 1, 4, 1, 1, 1, 1, 1, 1, 9, 19, 19, 19, 57, 9, 9, 9, 9, 9, 4, 1, 9, 9] 57 rigid atoms, others: [33, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35]) total number of confs: 116 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074747 none C[C@@H](O)C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [15, 7, 15, 15, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 9, 9, 9, 9, 1, 15, 15, 15, 45, 1, 1, 2, 2, 2, 5, 9, 1, 1] 57 rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 22, 27, 28] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 119 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074747 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074747 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074747/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074747 Building REAL250005074748 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074748' /scratch/stefan/7916156/working/building/REAL250005074748 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074748 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074748/0 /scratch/stefan/7916156/working/building/REAL250005074748 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 869) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/869 `/scratch/stefan/7916156/working/3D/869' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C1CC1C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074748.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074748/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074748 none C=C1CC1C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 10, 10, 10, 10, 1, 22, 22, 22, 22, 22, 1, 1, 2, 2, 2, 5, 10, 1, 1] 35 rigid atoms, others: [35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 22, 36, 28, 29] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34]) total number of confs: 79 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074748 none C=C1CC1C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 8, 8, 22, 22, 22, 22, 22, 22, 22, 31, 31, 31, 35, 35, 35, 35, 35, 22, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 31, 35, 22, 22] 35 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 25, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 82 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.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: REAL250005074748 none C=C1CC1C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 23, 10, 23, 10, 10, 10, 10, 10, 6, 10, 6, 1, 6, 1, 1, 1, 1, 1, 1, 10, 35, 35, 35, 35, 35, 10, 10, 10, 10, 10, 6, 1, 10, 10] 35 rigid atoms, others: [34, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36]) total number of confs: 105 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074748 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074748 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074748/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074748 Building REAL250005074749 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074749' /scratch/stefan/7916156/working/building/REAL250005074749 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074749 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074749/0 /scratch/stefan/7916156/working/building/REAL250005074749 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 870) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/870 `/scratch/stefan/7916156/working/3D/870' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC1C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074749.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074749.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074749/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074749 none CC1=CC1C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 13, 13, 13, 13, 1, 26, 26, 26, 26, 26, 1, 1, 2, 2, 2, 5, 13, 1, 1] 41 rigid atoms, others: [35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 22, 36, 28, 29] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34]) total number of confs: 93 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074749 none CC1=CC1C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 9, 9, 26, 26, 26, 26, 26, 26, 26, 36, 36, 36, 41, 41, 41, 41, 41, 26, 2, 2, 2, 1, 1, 26, 26, 26, 26, 26, 36, 41, 26, 26] 41 rigid atoms, others: [0, 1, 2, 3, 4, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 98 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.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: REAL250005074749 none CC1=CC1C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 22, 13, 22, 13, 13, 13, 13, 13, 6, 13, 6, 1, 6, 1, 1, 1, 1, 1, 1, 13, 41, 41, 41, 41, 41, 13, 13, 13, 13, 13, 6, 1, 13, 13] 41 rigid atoms, others: [34, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36]) total number of confs: 125 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074749 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074749 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074749/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074749 Building REAL250005074750 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074750' /scratch/stefan/7916156/working/building/REAL250005074750 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074750 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074750/0 /scratch/stefan/7916156/working/building/REAL250005074750 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 871) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/871 `/scratch/stefan/7916156/working/3D/871' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074750.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074750/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074750 none C=CC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 13, 20, 13, 13, 13, 13, 13, 7, 13, 7, 1, 7, 1, 1, 1, 1, 1, 1, 13, 20, 20, 20, 13, 13, 13, 13, 13, 8, 1, 13, 13] 20 rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32]) total number of confs: 57 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074750 none C=CC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 13, 13, 13, 13, 1, 11, 12, 12, 1, 1, 2, 2, 2, 5, 13, 1, 1] 20 rigid atoms, others: [32, 2, 4, 5, 6, 7, 8, 9, 10, 11, 20, 24, 25, 31] set([0, 1, 3, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 26, 27, 28, 29, 30]) total number of confs: 58 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074750 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074750 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074750/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074750 Building REAL250005074751 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074751' /scratch/stefan/7916156/working/building/REAL250005074751 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074751 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074751/0 /scratch/stefan/7916156/working/building/REAL250005074751 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 872) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/872 `/scratch/stefan/7916156/working/3D/872' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC(C)CC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005074751.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074751/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074751 none CC(=O)NC(C)CC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [74, 74, 74, 73, 62, 73, 31, 31, 31, 31, 11, 1, 11, 1, 1, 1, 1, 1, 1, 31, 31, 74, 74, 74, 74, 73, 73, 73, 73, 62, 62, 31, 31, 31, 31, 31, 1, 31, 31, 31, 31] 74 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: 290 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074751 none CC(=O)NC(C)CC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [19, 19, 19, 9, 5, 9, 1, 1, 1, 1, 1, 1, 7, 7, 31, 31, 31, 31, 31, 1, 1, 19, 19, 19, 19, 9, 9, 9, 9, 5, 5, 1, 1, 1, 1, 1, 31, 1, 1, 1, 1] 74 rigid atoms, others: [32, 33, 34, 35, 37, 6, 7, 8, 9, 10, 11, 40, 19, 20, 39, 38, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074751 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074751 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074751/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074751 Building REAL250005074752 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074752' /scratch/stefan/7916156/working/building/REAL250005074752 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074752 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074752/0 /scratch/stefan/7916156/working/building/REAL250005074752 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 873) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/873 `/scratch/stefan/7916156/working/3D/873' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC(CC(C)NC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005074752.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074752.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074752/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074752 none CC(=O)N1CCC(CC(C)NC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 43, 50, 43, 43, 43, 38, 22, 10, 22, 10, 1, 10, 1, 1, 1, 1, 1, 1, 43, 43, 50, 50, 50, 43, 43, 43, 43, 43, 38, 38, 22, 22, 22, 22, 10, 1, 43, 43, 43, 43] 50 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: 195 number of broken/clashed sets: 19 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074752 none CC(=O)N1CCC(CC(C)NC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 1, 5, 1, 1, 1, 1, 1, 5, 9, 9, 25, 25, 25, 43, 43, 43, 43, 43, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 9, 25, 43, 1, 1, 1, 1] 50 rigid atoms, others: [1, 3, 4, 5, 6, 7, 38, 39, 40, 19, 20, 24, 25, 26, 27, 28, 37] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 118 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074752 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074752 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074752/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074752 Building REAL250005074753 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074753' /scratch/stefan/7916156/working/building/REAL250005074753 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074753 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074753/0 /scratch/stefan/7916156/working/building/REAL250005074753 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 874) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/874 `/scratch/stefan/7916156/working/3D/874' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC1(C(C)(C)O)CN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074753.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074753/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074753 none CC(=O)NCC1(C(C)(C)O)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 12, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 144 conformations in input total number of sets (complete confs): 144 using faster count positions algorithm for large data unique positions, atoms: [47, 47, 47, 39, 22, 22, 22, 26, 26, 26, 22, 10, 1, 10, 1, 1, 1, 1, 1, 1, 22, 47, 47, 47, 47, 39, 39, 26, 26, 26, 26, 26, 26, 78, 22, 22, 1, 22, 22] 144 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: 231 number of broken/clashed sets: 111 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074753 none CC(=O)NCC1(C(C)(C)O)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 12, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 144 conformations in input total number of sets (complete confs): 144 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 9, 1, 1, 1, 4, 4, 4, 1, 1, 1, 7, 7, 22, 22, 22, 22, 22, 1, 17, 17, 17, 17, 9, 9, 4, 4, 4, 4, 4, 4, 12, 1, 1, 22, 1, 1] 144 rigid atoms, others: [34, 35, 4, 5, 6, 10, 11, 12, 20, 38, 37] set([0, 1, 2, 3, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36]) total number of confs: 106 number of broken/clashed sets: 111 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074753 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074753 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074753/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074753 Building REAL250005074754 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074754' /scratch/stefan/7916156/working/building/REAL250005074754 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074754 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074754/0 /scratch/stefan/7916156/working/building/REAL250005074754 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 875) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/875 `/scratch/stefan/7916156/working/3D/875' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC(CNC(=O)C2=CC(=O)[N-]O2)(C(C)(C)O)C1) `REAL250005074754.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074754/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074754 none CC(=O)N1CC(CNC(=O)C2=CC(=O)[N-]O2)(C(C)(C)O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 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 117 conformations in input total number of sets (complete confs): 117 using faster count positions algorithm for large data unique positions, atoms: [37, 30, 37, 30, 30, 17, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 30, 32, 32, 32, 30, 37, 37, 37, 30, 30, 16, 16, 6, 1, 32, 32, 32, 32, 32, 32, 96, 30, 30] 117 rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 230 number of broken/clashed sets: 77 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074754 none CC(=O)N1CC(CNC(=O)C2=CC(=O)[N-]O2)(C(C)(C)O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 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 117 conformations in input total number of sets (complete confs): 117 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 9, 21, 21, 21, 30, 30, 30, 30, 30, 1, 7, 7, 7, 1, 3, 3, 3, 1, 1, 9, 9, 21, 30, 7, 7, 7, 7, 7, 7, 21, 1, 1] 117 rigid atoms, others: [1, 3, 4, 5, 6, 16, 20, 24, 25, 38, 37] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 135 number of broken/clashed sets: 77 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074754 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074754 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074754/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074754 Building REAL250005074755 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074755' /scratch/stefan/7916156/working/building/REAL250005074755 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074755 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074755/0 /scratch/stefan/7916156/working/building/REAL250005074755 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 876) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/876 `/scratch/stefan/7916156/working/3D/876' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC(C2CCN(C(=O)C3=CC(=O)[N-]O3)C2)C1) `REAL250005074755.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074755.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074755/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074755 none CC(=O)N1CCC(C2CCN(C(=O)C3=CC(=O)[N-]O3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 12, 6, 6, 6, 1, 1, 1, 1, 1, 1, 5, 5, 15, 14, 15, 15, 15, 1, 6, 12, 12, 12, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 15, 1, 1, 6, 6] 31 rigid atoms, others: [32, 33, 35, 36, 6, 7, 8, 9, 10, 11, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 37, 38]) total number of confs: 63 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074755 none CC(=O)N1CCC(C2CCN(C(=O)C3=CC(=O)[N-]O3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 6, 6, 6, 6, 15, 15, 19, 19, 19, 19, 19, 6, 1, 4, 4, 4, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 19, 6, 6, 1, 1] 31 rigid atoms, others: [1, 3, 4, 5, 6, 7, 38, 20, 24, 25, 26, 27, 28, 37] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 60 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.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: REAL250005074755 none CC(=O)N1CCC(C2CCN(C(=O)C3=CC(=O)[N-]O3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 19, 31, 19, 19, 19, 15, 15, 15, 15, 8, 1, 8, 1, 1, 1, 1, 1, 1, 15, 19, 31, 31, 31, 19, 19, 19, 19, 19, 15, 15, 15, 15, 15, 1, 15, 15, 19, 19] 31 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: 91 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074755 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074755 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074755/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074755 Building REAL250005074756 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074756' /scratch/stefan/7916156/working/building/REAL250005074756 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074756 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074756/0 /scratch/stefan/7916156/working/building/REAL250005074756 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 877) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/877 `/scratch/stefan/7916156/working/3D/877' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC(C2CCN(C(=O)C3=CC(=O)[N-]O3)C2)C1) `REAL250005074756.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074756/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074756 none CC(=O)N1CCC(C2CCN(C(=O)C3=CC(=O)[N-]O3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 12, 6, 6, 6, 1, 1, 1, 1, 1, 1, 5, 5, 15, 14, 15, 15, 15, 1, 6, 12, 12, 12, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 15, 1, 1, 6, 6] 31 rigid atoms, others: [32, 33, 35, 36, 6, 7, 8, 9, 10, 11, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 37, 38]) total number of confs: 63 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074756 none CC(=O)N1CCC(C2CCN(C(=O)C3=CC(=O)[N-]O3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 6, 6, 6, 6, 15, 15, 19, 19, 19, 19, 19, 6, 1, 4, 4, 4, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 19, 6, 6, 1, 1] 31 rigid atoms, others: [1, 3, 4, 5, 6, 7, 38, 20, 24, 25, 26, 27, 28, 37] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 60 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.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: REAL250005074756 none CC(=O)N1CCC(C2CCN(C(=O)C3=CC(=O)[N-]O3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 19, 31, 19, 19, 19, 15, 15, 15, 15, 8, 1, 8, 1, 1, 1, 1, 1, 1, 15, 19, 31, 31, 31, 19, 19, 19, 19, 19, 15, 15, 15, 15, 15, 1, 15, 15, 19, 19] 31 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: 91 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074756 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074756 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074756/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074756 Building REAL250005074757 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074757' /scratch/stefan/7916156/working/building/REAL250005074757 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074757 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074757/0 /scratch/stefan/7916156/working/building/REAL250005074757 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 878) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/878 `/scratch/stefan/7916156/working/3D/878' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC1CCCC2CN(C(=O)C3=CC(=O)[N-]O3)CC21) `REAL250005074757.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074757/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074757 none CC(=O)NC1CCCC2CN(C(=O)C3=CC(=O)[N-]O3)CC21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 17, 17, 18, 18, 18, 18, 18, 8, 1, 8, 1, 1, 1, 1, 1, 1, 17, 17, 22, 22, 22, 22, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 17, 17, 18] 22 rigid atoms, others: [35, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38]) total number of confs: 55 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074757 none CC(=O)NC1CCCC2CN(C(=O)C3=CC(=O)[N-]O3)CC21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 17, 17, 17, 18, 18, 1, 1, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1] 22 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38] set([0, 1, 2, 35, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074757 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074757 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074757/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074757 Building REAL250005074758 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074758' /scratch/stefan/7916156/working/building/REAL250005074758 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074758 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074758/0 /scratch/stefan/7916156/working/building/REAL250005074758 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 879) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/879 `/scratch/stefan/7916156/working/3D/879' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC2CCCC(NC(=O)C3=CC(=O)[N-]O3)C2C1) `REAL250005074758.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074758/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074758 none CC(=O)N1CC2CCCC(NC(=O)C3=CC(=O)[N-]O3)C2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [11, 8, 11, 8, 8, 8, 8, 8, 8, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 8, 8, 11, 11, 11, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 1, 8, 8, 8] 11 rigid atoms, others: [35, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38]) total number of confs: 31 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074758 none CC(=O)N1CC2CCCC(NC(=O)C3=CC(=O)[N-]O3)C2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 8, 8, 8, 8, 8, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 8, 1, 1, 1] 11 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38] set([0, 2, 34, 11, 12, 13, 14, 15, 16, 17, 18, 35, 21, 22, 23]) total number of confs: 28 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074758 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074758 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074758/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074758 Building REAL250005074759 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074759' /scratch/stefan/7916156/working/building/REAL250005074759 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074759 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074759/0 /scratch/stefan/7916156/working/building/REAL250005074759 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 880) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/880 `/scratch/stefan/7916156/working/3D/880' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NCC1CN(C(=O)C2=CC(=O)[N-]O2)CCC1C) `REAL250005074759.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074759/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074759 none CCC(=O)NCC1CN(C(=O)C2=CC(=O)[N-]O2)CCC1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 136 conformations in input total number of sets (complete confs): 136 using faster count positions algorithm for large data unique positions, atoms: [136, 99, 99, 99, 54, 28, 28, 28, 10, 1, 10, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 136, 136, 136, 136, 136, 99, 54, 54, 28, 28, 28, 1, 28, 28, 28, 28, 28, 28, 28, 28] 136 rigid atoms, others: [32, 9, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 533 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074759 none CCC(=O)NCC1CN(C(=O)C2=CC(=O)[N-]O2)CCC1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 136 conformations in input total number of sets (complete confs): 136 using faster count positions algorithm for large data unique positions, atoms: [74, 20, 20, 20, 6, 1, 1, 1, 1, 1, 7, 7, 28, 28, 28, 28, 28, 1, 1, 1, 1, 74, 74, 74, 74, 74, 20, 6, 6, 1, 1, 1, 28, 1, 1, 1, 1, 1, 2, 2, 2] 136 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 17, 18, 19, 20, 37, 29, 30, 31] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 32, 38, 39, 40]) total number of confs: 309 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074759 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074759 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074759/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074759 Building REAL250005074760 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074760' /scratch/stefan/7916156/working/building/REAL250005074760 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074760 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074760/0 /scratch/stefan/7916156/working/building/REAL250005074760 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 881) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/881 `/scratch/stefan/7916156/working/3D/881' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC1CN(C(=O)C2=CC(=O)[N-]O2)CCC1C) `REAL250005074760.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074760/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074760 none CC(=O)NCC1CN(C(=O)C2=CC(=O)[N-]O2)CCC1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 34, 23, 23, 23, 10, 1, 10, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 49, 49, 49, 49, 34, 34, 23, 23, 23, 1, 23, 23, 23, 23, 23, 23, 23, 23] 49 rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 160 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074760 none CC(=O)NCC1CN(C(=O)C2=CC(=O)[N-]O2)CCC1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 4, 1, 1, 1, 1, 1, 7, 7, 23, 23, 23, 23, 23, 1, 1, 1, 1, 16, 16, 16, 16, 4, 4, 1, 1, 1, 23, 1, 1, 1, 1, 1, 2, 2, 2] 49 rigid atoms, others: [32, 33, 34, 4, 5, 6, 7, 8, 16, 17, 18, 19, 26, 27, 28, 30, 31] set([0, 1, 2, 3, 36, 37, 9, 10, 11, 12, 13, 14, 15, 35, 20, 21, 22, 23, 24, 25, 29]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074760 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074760 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074760/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074760 Building REAL250005074761 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074761' /scratch/stefan/7916156/working/building/REAL250005074761 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074761 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074761/0 /scratch/stefan/7916156/working/building/REAL250005074761 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 882) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/882 `/scratch/stefan/7916156/working/3D/882' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1CNC(=O)CO) `REAL250005074761.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074761/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074761 none CC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1CNC(=O)CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 8, 1, 11, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 351 conformations in input total number of sets (complete confs): 351 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 36, 36, 11, 1, 11, 1, 1, 1, 1, 1, 1, 36, 36, 36, 72, 117, 117, 117, 116, 36, 36, 36, 36, 36, 36, 36, 36, 1, 36, 36, 36, 72, 72, 117, 117, 117, 351] 351 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 736 number of broken/clashed sets: 15 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074761 none CC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1CNC(=O)CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 8, 1, 11, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 351 conformations in input total number of sets (complete confs): 351 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 36, 36, 36, 36, 36, 1, 1, 1, 6, 24, 24, 24, 56, 2, 2, 2, 1, 1, 1, 1, 1, 36, 1, 1, 1, 6, 6, 24, 58, 58, 174] 351 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 13, 14, 15, 24, 25, 26, 27, 28, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 29, 33, 34, 35, 36, 37, 38]) total number of confs: 437 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074761 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074761 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074761/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074761 Building REAL250005074762 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074762' /scratch/stefan/7916156/working/building/REAL250005074762 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074762 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074762/0 /scratch/stefan/7916156/working/building/REAL250005074762 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 883) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/883 `/scratch/stefan/7916156/working/3D/883' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N1CCC(C)C(CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074762.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074762/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074762 none CCC(=O)N1CCC(C)C(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [72, 72, 40, 72, 40, 40, 40, 40, 40, 19, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 40, 72, 72, 72, 72, 72, 40, 40, 40, 40, 40, 40, 40, 40, 40, 19, 19, 5, 1, 40, 40] 72 rigid atoms, others: [38, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40]) total number of confs: 227 number of broken/clashed sets: 18 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074762 none CCC(=O)N1CCC(C)C(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [17, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 8, 33, 33, 33, 40, 40, 40, 40, 40, 1, 18, 18, 18, 17, 17, 1, 1, 1, 1, 1, 2, 2, 2, 1, 8, 8, 33, 40, 1, 1] 72 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 39, 34, 40, 20, 26, 27, 28, 29, 30] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 31, 32, 33, 35, 36, 37, 38]) total number of confs: 173 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074762 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074762 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074762/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074762 Building REAL250005074763 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074763' /scratch/stefan/7916156/working/building/REAL250005074763 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074763 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074763/0 /scratch/stefan/7916156/working/building/REAL250005074763 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 884) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/884 `/scratch/stefan/7916156/working/3D/884' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC(C)C(CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074763.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074763/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074763 none CC(=O)N1CCC(C)C(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [43, 33, 43, 33, 33, 33, 33, 33, 19, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 33, 43, 43, 43, 33, 33, 33, 33, 33, 33, 33, 33, 33, 19, 19, 8, 1, 33, 33] 43 rigid atoms, others: [35, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37]) total number of confs: 145 number of broken/clashed sets: 24 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074763 none CC(=O)N1CCC(C)C(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 7, 26, 26, 26, 33, 33, 33, 33, 33, 1, 5, 5, 5, 1, 1, 1, 1, 1, 2, 2, 2, 1, 7, 7, 26, 33, 1, 1] 43 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 19, 23, 24, 25, 26, 27, 36, 37, 31] set([0, 32, 2, 34, 33, 10, 11, 12, 13, 14, 15, 16, 17, 18, 35, 20, 21, 22, 28, 29, 30]) total number of confs: 101 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074763 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074763 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074763/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074763 Building REAL250005074764 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074764' /scratch/stefan/7916156/working/building/REAL250005074764 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074764 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074764/0 /scratch/stefan/7916156/working/building/REAL250005074764 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 885) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/885 `/scratch/stefan/7916156/working/3D/885' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCN(C(=O)CO)CC1CNC(=O)C1=CC(=O)[N-]O1) `REAL250005074764.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074764/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074764 none CC1CCN(C(=O)CO)CC1CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 156 conformations in input total number of sets (complete confs): 156 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 35, 35, 35, 35, 51, 51, 52, 35, 20, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 35, 35, 35, 35, 52, 52, 156, 35, 35, 35, 20, 20, 7, 1] 156 rigid atoms, others: [38, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 336 number of broken/clashed sets: 49 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074764 none CC1CCN(C(=O)CO)CC1CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 156 conformations in input total number of sets (complete confs): 156 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 13, 1, 1, 1, 6, 25, 25, 25, 35, 35, 35, 35, 35, 2, 2, 2, 1, 1, 1, 1, 1, 13, 13, 39, 1, 1, 1, 6, 6, 25, 35] 156 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 9, 10, 11, 34, 33, 24, 25, 26, 27, 28] set([6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 35, 36, 37, 38]) total number of confs: 176 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074764 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074764 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074764/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074764 Building REAL250005074765 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074765' /scratch/stefan/7916156/working/building/REAL250005074765 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074765 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074765/0 /scratch/stefan/7916156/working/building/REAL250005074765 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 886) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/886 `/scratch/stefan/7916156/working/3D/886' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(=O)N1CCC(C)C(CNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074765.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074765/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074765 none C=CC(=O)N1CCC(C)C(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [62, 62, 42, 62, 42, 42, 42, 42, 42, 22, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 42, 62, 62, 62, 42, 42, 42, 42, 42, 42, 42, 42, 42, 21, 21, 6, 1, 42, 42] 62 rigid atoms, others: [36, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 197 number of broken/clashed sets: 15 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074765 none C=CC(=O)N1CCC(C)C(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [24, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 7, 30, 30, 30, 42, 42, 42, 42, 42, 1, 24, 24, 24, 1, 1, 1, 1, 1, 2, 2, 2, 1, 7, 7, 30, 42, 1, 1] 62 rigid atoms, others: [32, 2, 4, 5, 6, 7, 8, 9, 10, 38, 20, 24, 25, 26, 27, 28, 37] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 29, 30, 31, 33, 34, 35, 36]) total number of confs: 166 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074765 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074765 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074765/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074765 Building REAL250005074766 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074766' /scratch/stefan/7916156/working/building/REAL250005074766 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074766 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074766/0 /scratch/stefan/7916156/working/building/REAL250005074766 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 887) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/887 `/scratch/stefan/7916156/working/3D/887' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NCC12CCC1CCN2C(=O)C1=CC(=O)[N-]O1) `REAL250005074766.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074766.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074766/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074766 none CCC(=O)NCC12CCC1CCN2C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [88, 76, 76, 76, 52, 24, 24, 24, 24, 24, 24, 24, 10, 1, 10, 1, 1, 1, 1, 1, 1, 88, 88, 88, 88, 88, 76, 52, 52, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1] 88 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: 331 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074766 none CCC(=O)NCC12CCC1CCN2C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [57, 17, 17, 17, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 24, 24, 24, 24, 24, 57, 57, 57, 57, 57, 17, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24] 88 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 12, 13, 37, 29, 30, 31] set([0, 1, 2, 3, 4, 38, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 243 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074766 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074766 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074766/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074766 Building REAL250005074767 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074767' /scratch/stefan/7916156/working/building/REAL250005074767 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074767 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074767/0 /scratch/stefan/7916156/working/building/REAL250005074767 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 888) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/888 `/scratch/stefan/7916156/working/3D/888' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC12CCC1CCN2C(=O)C1=CC(=O)[N-]O1) `REAL250005074767.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074767/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074767 none CC(=O)NCC12CCC1CCN2C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 29, 17, 17, 17, 17, 17, 17, 17, 10, 1, 10, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 29, 29, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1] 31 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: 104 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074767 none CC(=O)NCC12CCC1CCN2C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 17, 17, 17, 17, 17, 13, 13, 13, 13, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17] 31 rigid atoms, others: [32, 33, 34, 4, 5, 6, 7, 8, 9, 10, 11, 12, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 35, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074767 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074767 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074767/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074767 Building REAL250005074768 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074768' /scratch/stefan/7916156/working/building/REAL250005074768 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074768 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074768/0 /scratch/stefan/7916156/working/building/REAL250005074768 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 889) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/889 `/scratch/stefan/7916156/working/3D/889' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CO)NCC12CCC1CCN2C(=O)C1=CC(=O)[N-]O1) `REAL250005074768.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074768.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074768/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074768 none O=C(CO)NCC12CCC1CCN2C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 54, 54, 37, 17, 17, 17, 17, 17, 17, 17, 8, 1, 8, 1, 1, 1, 1, 1, 1, 54, 54, 162, 54, 37, 37, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1] 162 rigid atoms, others: [36, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 350 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074768 none O=C(CO)NCC12CCC1CCN2C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 39, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 17, 17, 17, 17, 17, 39, 39, 117, 22, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17] 162 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 10, 11, 12, 13, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36]) total number of confs: 282 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074768 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074768 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074768/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074768 Building REAL250005074769 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074769' /scratch/stefan/7916156/working/building/REAL250005074769 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074769 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074769/0 /scratch/stefan/7916156/working/building/REAL250005074769 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 890) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/890 `/scratch/stefan/7916156/working/3D/890' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N1CCC2CCC21CNC(=O)C1=CC(=O)[N-]O1) `REAL250005074769.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074769/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074769 none CCC(=O)N1CCC2CCC21CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 31, 39, 31, 31, 31, 31, 31, 31, 20, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39, 31, 31, 31, 31, 31, 31, 31, 31, 31, 20, 20, 9, 1] 39 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: 114 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074769 none CCC(=O)N1CCC2CCC21CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [14, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 7, 21, 21, 21, 31, 31, 31, 31, 31, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 21, 31] 39 rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 9, 10, 11, 34, 26, 27, 28, 29, 30, 31] set([0, 1, 3, 36, 37, 35, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 38]) total number of confs: 116 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074769 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074769 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074769/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074769 Building REAL250005074770 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074770' /scratch/stefan/7916156/working/building/REAL250005074770 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074770 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074770/0 /scratch/stefan/7916156/working/building/REAL250005074770 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 891) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/891 `/scratch/stefan/7916156/working/3D/891' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC2CCC21CNC(=O)C1=CC(=O)[N-]O1) `REAL250005074770.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074770/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074770 none CC(=O)N1CCC2CCC21CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 23, 28, 23, 23, 23, 23, 23, 23, 15, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 28, 28, 28, 23, 23, 23, 23, 23, 23, 23, 23, 23, 15, 15, 7, 1] 28 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: 84 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074770 none CC(=O)N1CCC2CCC21CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 20, 20, 20, 23, 23, 23, 23, 23, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 20, 23] 28 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 32, 2, 34, 35, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22]) total number of confs: 74 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074770 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074770 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074770/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074770 Building REAL250005074771 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074771' /scratch/stefan/7916156/working/building/REAL250005074771 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074771 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074771/0 /scratch/stefan/7916156/working/building/REAL250005074771 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 892) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/892 `/scratch/stefan/7916156/working/3D/892' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CO)N1CCC2CCC21CNC(=O)C1=CC(=O)[N-]O1) `REAL250005074771.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074771/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074771 none O=C(CO)N1CCC2CCC21CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [21, 18, 21, 24, 18, 18, 18, 18, 18, 18, 12, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 24, 24, 72, 18, 18, 18, 18, 18, 18, 18, 18, 18, 12, 12, 6, 1] 72 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: 146 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074771 none O=C(CO)N1CCC2CCC21CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 10, 1, 1, 1, 1, 1, 1, 1, 1, 5, 14, 14, 14, 18, 18, 18, 18, 18, 10, 10, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 14, 18] 72 rigid atoms, others: [32, 1, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 33, 2, 3, 36, 35, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 34]) total number of confs: 110 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074771 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074771 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074771/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074771 Building REAL250005074772 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074772' /scratch/stefan/7916156/working/building/REAL250005074772 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074772 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074772/0 /scratch/stefan/7916156/working/building/REAL250005074772 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 893) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/893 `/scratch/stefan/7916156/working/3D/893' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(=O)N1CCC2CCC21CNC(=O)C1=CC(=O)[N-]O1) `REAL250005074772.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074772/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074772 none C=CC(=O)N1CCC2CCC21CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 26, 31, 26, 26, 26, 26, 26, 26, 17, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 31, 31, 31, 26, 26, 26, 26, 26, 26, 26, 26, 26, 17, 17, 8, 1] 31 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: 86 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074772 none C=CC(=O)N1CCC2CCC21CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 18, 18, 18, 26, 26, 26, 26, 26, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 18, 26] 31 rigid atoms, others: [32, 2, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 34, 3, 36, 35, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23]) total number of confs: 95 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074772 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074772 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074772/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074772 Building REAL250005074773 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074773' /scratch/stefan/7916156/working/building/REAL250005074773 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074773 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074773/0 /scratch/stefan/7916156/working/building/REAL250005074773 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 894) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/894 `/scratch/stefan/7916156/working/3D/894' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC(C2CCCN2C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074773.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074773/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074773 none CC(=O)N1CCC(C2CCCN2C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 4, 6, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 10, 11, 10, 10, 4, 6, 6, 6, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 11, 4, 4] 19 rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 11, 12, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36, 37, 38]) total number of confs: 38 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074773 none CC(=O)N1CCC(C2CCCN2C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 2, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 9, 9, 14, 14, 14, 14, 14, 1, 3, 3, 3, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 14, 1, 1] 19 rigid atoms, others: [1, 3, 4, 5, 6, 7, 38, 20, 24, 25, 26, 27, 28, 37] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074773 none CC(=O)N1CCC(C2CCCN2C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 14, 19, 14, 14, 14, 11, 11, 11, 11, 11, 5, 1, 5, 1, 1, 1, 1, 1, 1, 14, 19, 19, 19, 14, 14, 14, 14, 14, 11, 11, 11, 11, 11, 11, 11, 1, 14, 14] 19 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: 52 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074773 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074773 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074773/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074773 Building REAL250005074774 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074774' /scratch/stefan/7916156/working/building/REAL250005074774 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074774 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074774/0 /scratch/stefan/7916156/working/building/REAL250005074774 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 895) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/895 `/scratch/stefan/7916156/working/3D/895' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCCC1C1CCN(C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074774.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074774/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074774 none CC(=O)N1CCCC1C1CCN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 7, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 6, 6, 12, 12, 12, 12, 12, 1, 7, 7, 7, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 12, 1, 1] 21 rigid atoms, others: [32, 33, 34, 35, 37, 38, 7, 8, 9, 10, 11, 12, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36]) total number of confs: 40 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074774 none CC(=O)N1CCCC1C1CCN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 12, 12, 16, 16, 16, 16, 16, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 16, 4, 4] 21 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 24, 25, 26, 27, 28, 29, 30] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 44 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.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: REAL250005074774 none CC(=O)N1CCCC1C1CCN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 16, 21, 16, 16, 16, 16, 12, 12, 12, 12, 8, 1, 8, 1, 1, 1, 1, 1, 1, 12, 21, 21, 21, 16, 16, 16, 16, 16, 16, 16, 12, 12, 12, 12, 12, 1, 12, 12] 21 rigid atoms, others: [36, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 60 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074774 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074774 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074774/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074774 Building REAL250005074775 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074775' /scratch/stefan/7916156/working/building/REAL250005074775 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074775 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074775/0 /scratch/stefan/7916156/working/building/REAL250005074775 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 896) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/896 `/scratch/stefan/7916156/working/3D/896' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NC(C)C1CN(C(=O)C2=CC(=O)[N-]O2)CCO1) `REAL250005074775.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074775.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074775/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074775 none CCC(=O)NC(C)C1CN(C(=O)C2=CC(=O)[N-]O2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 92 conformations in input total number of sets (complete confs): 92 using faster count positions algorithm for large data unique positions, atoms: [92, 62, 62, 62, 45, 24, 45, 24, 24, 9, 1, 9, 1, 1, 1, 1, 1, 1, 24, 24, 24, 92, 92, 92, 92, 92, 62, 45, 45, 45, 45, 24, 24, 24, 1, 24, 24, 24, 24] 92 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: 390 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074775 none CCC(=O)NC(C)C1CN(C(=O)C2=CC(=O)[N-]O2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 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: [46, 15, 15, 15, 7, 1, 7, 1, 1, 1, 1, 7, 7, 24, 24, 24, 24, 24, 1, 1, 1, 46, 46, 46, 46, 46, 15, 7, 7, 7, 7, 1, 1, 1, 24, 1, 1, 1, 1] 92 rigid atoms, others: [32, 33, 35, 36, 5, 38, 7, 8, 9, 10, 18, 19, 20, 37, 31] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34]) total number of confs: 214 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074775 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074775 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074775/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074775 Building REAL250005074776 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074776' /scratch/stefan/7916156/working/building/REAL250005074776 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074776 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074776/0 /scratch/stefan/7916156/working/building/REAL250005074776 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 897) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/897 `/scratch/stefan/7916156/working/3D/897' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC(C)C1CN(C(=O)C2=CC(=O)[N-]O2)CCO1) `REAL250005074776.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074776.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074776/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074776 none CC(=O)NC(C)C1CN(C(=O)C2=CC(=O)[N-]O2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', '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, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 43, 17, 43, 17, 17, 9, 1, 9, 1, 1, 1, 1, 1, 1, 17, 17, 17, 47, 47, 47, 47, 43, 43, 43, 43, 17, 17, 17, 1, 17, 17, 17, 17] 47 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: 151 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074776 none CC(=O)NC(C)C1CN(C(=O)C2=CC(=O)[N-]O2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', '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, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 8, 1, 8, 1, 1, 1, 1, 7, 7, 17, 17, 17, 17, 17, 1, 1, 1, 14, 14, 14, 14, 8, 8, 8, 8, 1, 1, 1, 17, 1, 1, 1, 1] 47 rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 17, 18, 19, 28, 29, 30] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 74 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074776 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074776 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074776/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074776 Building REAL250005074777 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074777' /scratch/stefan/7916156/working/building/REAL250005074777 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074777 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074777/0 /scratch/stefan/7916156/working/building/REAL250005074777 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 898) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/898 `/scratch/stefan/7916156/working/3D/898' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(NC(=O)CO)C1CN(C(=O)C2=CC(=O)[N-]O2)CCO1) `REAL250005074777.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074777/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074777 none CC(NC(=O)CO)C1CN(C(=O)C2=CC(=O)[N-]O2)CCO1 NO_LONG_NAME dock atom types: ['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', '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, 8, 1, 11, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 216 conformations in input total number of sets (complete confs): 216 using faster count positions algorithm for large data unique positions, atoms: [67, 32, 67, 72, 72, 72, 72, 32, 32, 11, 1, 11, 1, 1, 1, 1, 1, 1, 32, 32, 32, 67, 67, 67, 67, 72, 72, 72, 216, 32, 32, 32, 1, 32, 32, 32, 32] 216 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: 445 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074777 none CC(NC(=O)CO)C1CN(C(=O)C2=CC(=O)[N-]O2)CCO1 NO_LONG_NAME dock atom types: ['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', '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, 8, 1, 11, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 216 conformations in input total number of sets (complete confs): 216 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 17, 17, 17, 33, 1, 1, 1, 1, 7, 7, 32, 32, 32, 32, 32, 1, 1, 1, 9, 9, 9, 9, 17, 33, 33, 99, 1, 1, 1, 32, 1, 1, 1, 1] 216 rigid atoms, others: [1, 34, 35, 36, 33, 7, 8, 9, 10, 18, 19, 20, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 32]) total number of confs: 264 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074777 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074777 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074777/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074777 Building REAL250005074778 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074778' /scratch/stefan/7916156/working/building/REAL250005074778 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074778 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074778/0 /scratch/stefan/7916156/working/building/REAL250005074778 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 899) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/899 `/scratch/stefan/7916156/working/3D/899' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N1CCOC(C(C)NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074778.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074778/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074778 none CCC(=O)N1CCOC(C(C)NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 12, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 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, 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, 45, 30, 45, 30, 30, 30, 30, 14, 5, 14, 5, 1, 5, 1, 1, 1, 1, 1, 1, 30, 46, 46, 46, 46, 46, 30, 30, 30, 30, 30, 14, 14, 14, 14, 6, 1, 30, 30] 46 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: 152 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074778 none CCC(=O)N1CCOC(C(C)NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 12, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 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, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 1, 6, 1, 1, 1, 1, 1, 1, 8, 8, 22, 22, 22, 30, 30, 30, 30, 30, 1, 15, 15, 15, 14, 14, 1, 1, 1, 1, 1, 8, 8, 8, 8, 22, 30, 1, 1] 46 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 38, 20, 26, 27, 28, 29, 30, 37] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 31, 32, 33, 34, 35, 36]) total number of confs: 133 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074778 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074778 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074778/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074778 Building REAL250005074779 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074779' /scratch/stefan/7916156/working/building/REAL250005074779 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074779 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074779/0 /scratch/stefan/7916156/working/building/REAL250005074779 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 900) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/900 `/scratch/stefan/7916156/working/3D/900' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCOC(C(C)NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074779.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074779/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074779 none CC(=O)N1CCOC(C(C)NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 12, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 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] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [25, 22, 25, 22, 22, 22, 22, 13, 5, 13, 5, 1, 5, 1, 1, 1, 1, 1, 1, 22, 25, 25, 25, 22, 22, 22, 22, 22, 13, 13, 13, 13, 5, 1, 22, 22] 25 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: 87 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074779 none CC(=O)N1CCOC(C(C)NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 12, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 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] 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: [5, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 15, 15, 15, 22, 22, 22, 22, 22, 1, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 7, 15, 22, 1, 1] 25 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 19, 23, 24, 25, 26, 27, 35] set([0, 32, 2, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 28, 29, 30, 31]) total number of confs: 69 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074779 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074779 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074779/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074779 Building REAL250005074780 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074780' /scratch/stefan/7916156/working/building/REAL250005074780 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074780 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074780/0 /scratch/stefan/7916156/working/building/REAL250005074780 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 901) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/901 `/scratch/stefan/7916156/working/3D/901' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)CO)CCO1) `REAL250005074780.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074780.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074780/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074780 none CC(NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)CO)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 17, 17, 17, 30, 30, 30, 30, 30, 1, 1, 1, 1, 4, 4, 13, 1, 1, 1, 5, 5, 5, 5, 17, 30, 1, 1, 1, 13, 13, 39, 1, 1, 1, 1] 108 rigid atoms, others: [1, 34, 35, 36, 33, 11, 12, 13, 14, 18, 19, 20, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 17, 21, 22, 23, 24, 25, 26, 30, 31, 32]) total number of confs: 150 number of broken/clashed sets: 24 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074780 none CC(NC(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)CO)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [15, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 15, 30, 30, 30, 35, 35, 36, 30, 30, 30, 15, 15, 15, 15, 8, 1, 30, 30, 30, 36, 36, 108, 30, 30, 30, 30] 108 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 26] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 227 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074780 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074780 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074780/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074780 Building REAL250005074781 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074781' /scratch/stefan/7916156/working/building/REAL250005074781 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074781 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074781/0 /scratch/stefan/7916156/working/building/REAL250005074781 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 902) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/902 `/scratch/stefan/7916156/working/3D/902' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(=O)N1CCOC(C(C)NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074781.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074781/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074781 none C=CC(=O)N1CCOC(C(C)NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 12, 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, 6, 7, 7, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 25, 37, 25, 25, 25, 25, 10, 4, 10, 4, 1, 4, 1, 1, 1, 1, 1, 1, 25, 37, 37, 37, 25, 25, 25, 25, 25, 10, 10, 10, 10, 5, 1, 25, 25] 37 rigid atoms, others: [34, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36]) total number of confs: 122 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074781 none C=CC(=O)N1CCOC(C(C)NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 12, 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, 6, 7, 7, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [19, 7, 1, 7, 1, 1, 1, 1, 1, 1, 8, 8, 21, 21, 21, 25, 25, 25, 25, 25, 1, 19, 19, 19, 1, 1, 1, 1, 1, 8, 8, 8, 8, 21, 25, 1, 1] 37 rigid atoms, others: [2, 35, 4, 5, 6, 7, 8, 9, 20, 24, 25, 26, 27, 28, 36] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 29, 30, 31, 32, 33, 34]) total number of confs: 119 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074781 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074781 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074781/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074781 Building REAL250005074782 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074782' /scratch/stefan/7916156/working/building/REAL250005074782 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074782 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074782/0 /scratch/stefan/7916156/working/building/REAL250005074782 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 903) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/903 `/scratch/stefan/7916156/working/3D/903' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NC[C@@H]1C[C@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@@H]12) `REAL250005074782.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074782/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074782 none CCC(=O)NC[C@@H]1C[C@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@@H]12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 170, 170, 170, 86, 28, 28, 28, 28, 28, 28, 28, 10, 1, 10, 1, 1, 1, 1, 1, 1, 28, 28, 28, 201, 201, 201, 201, 201, 170, 86, 86, 28, 28, 28, 28, 1, 28, 28] 201 rigid atoms, others: [36, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 729 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074782 none CCC(=O)NC[C@@H]1C[C@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@@H]12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [133, 43, 43, 43, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 28, 28, 28, 28, 28, 1, 1, 1, 133, 133, 133, 133, 133, 43, 7, 7, 1, 1, 1, 1, 28, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 38, 37] set([0, 1, 2, 3, 4, 36, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 516 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074782 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074782 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074782/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074782 Building REAL250005074783 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074783' /scratch/stefan/7916156/working/building/REAL250005074783 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074783 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074783/0 /scratch/stefan/7916156/working/building/REAL250005074783 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 904) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/904 `/scratch/stefan/7916156/working/3D/904' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC[C@@H]1C[C@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@@H]12) `REAL250005074783.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074783.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074783/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074783 none CC(=O)NC[C@@H]1C[C@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@@H]12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', '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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [76, 76, 76, 63, 28, 28, 28, 28, 28, 28, 28, 10, 1, 10, 1, 1, 1, 1, 1, 1, 28, 28, 28, 76, 76, 76, 76, 63, 63, 28, 28, 28, 28, 1, 28, 28] 76 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: 257 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074783 none CC(=O)NC[C@@H]1C[C@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@@H]12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', '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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 36, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 28, 28, 28, 28, 28, 1, 1, 1, 36, 36, 36, 36, 8, 8, 1, 1, 1, 1, 28, 1, 1] 76 rigid atoms, others: [32, 34, 35, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 33, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28]) total number of confs: 135 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074783 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074783 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074783/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074783 Building REAL250005074784 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074784' /scratch/stefan/7916156/working/building/REAL250005074784 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074784 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074784/0 /scratch/stefan/7916156/working/building/REAL250005074784 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 905) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/905 `/scratch/stefan/7916156/working/3D/905' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CO)NC[C@@H]1C[C@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@@H]12) `REAL250005074784.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074784/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074784 none O=C(CO)NC[C@@H]1C[C@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@@H]12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [121, 121, 121, 123, 79, 30, 30, 30, 30, 30, 30, 30, 10, 1, 10, 1, 1, 1, 1, 1, 1, 30, 30, 30, 123, 123, 369, 121, 79, 79, 30, 30, 30, 30, 1, 30, 30] 369 rigid atoms, others: [34, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36]) total number of confs: 782 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074784 none O=C(CO)NC[C@@H]1C[C@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@@H]12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [39, 39, 39, 84, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 30, 30, 30, 30, 30, 1, 1, 1, 84, 84, 252, 39, 7, 7, 1, 1, 1, 1, 30, 1, 1] 369 rigid atoms, others: [32, 33, 35, 36, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 34, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29]) total number of confs: 597 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074784 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074784 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074784/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074784 Building REAL250005074785 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074785' /scratch/stefan/7916156/working/building/REAL250005074785 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074785 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074785/0 /scratch/stefan/7916156/working/building/REAL250005074785 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 906) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/906 `/scratch/stefan/7916156/working/3D/906' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N1C[C@@H]2C[C@@H](CNC(=O)C3=CC(=O)[N-]O3)[C@@H]2C1) `REAL250005074785.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074785/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074785 none CCC(=O)N1C[C@@H]2C[C@@H](CNC(=O)C3=CC(=O)[N-]O3)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [123, 112, 80, 112, 80, 80, 80, 80, 80, 42, 80, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 80, 80, 80, 123, 123, 123, 123, 123, 80, 80, 80, 80, 41, 41, 7, 1, 80, 80] 123 rigid atoms, others: [36, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 436 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074785 none CCC(=O)N1C[C@@H]2C[C@@H](CNC(=O)C3=CC(=O)[N-]O3)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [20, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 9, 47, 47, 47, 80, 80, 80, 80, 80, 1, 1, 1, 21, 21, 21, 20, 20, 1, 1, 1, 1, 9, 9, 47, 80, 1, 1] 123 rigid atoms, others: [32, 2, 4, 5, 6, 7, 8, 9, 10, 11, 37, 21, 22, 23, 38, 29, 30, 31] set([0, 1, 34, 3, 36, 35, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28]) total number of confs: 245 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074785 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074785 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074785/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074785 Building REAL250005074786 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074786' /scratch/stefan/7916156/working/building/REAL250005074786 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074786 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074786/0 /scratch/stefan/7916156/working/building/REAL250005074786 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 907) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/907 `/scratch/stefan/7916156/working/3D/907' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1C[C@@H]2C[C@@H](CNC(=O)C3=CC(=O)[N-]O3)[C@@H]2C1) `REAL250005074786.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074786/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074786 none CC(=O)N1C[C@@H]2C[C@@H](CNC(=O)C3=CC(=O)[N-]O3)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [52, 37, 52, 37, 37, 37, 37, 37, 26, 37, 8, 7, 1, 7, 1, 1, 1, 1, 1, 1, 37, 37, 37, 52, 52, 52, 37, 37, 37, 37, 26, 26, 8, 1, 37, 37] 52 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: 187 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074786 none CC(=O)N1C[C@@H]2C[C@@H](CNC(=O)C3=CC(=O)[N-]O3)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 9, 29, 29, 29, 37, 37, 37, 37, 37, 1, 1, 1, 3, 3, 3, 1, 1, 1, 1, 9, 9, 29, 37, 1, 1] 52 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 9, 10, 35, 20, 21, 22, 26, 27, 28, 29] set([0, 32, 2, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 30, 31]) total number of confs: 105 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074786 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074786 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074786/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074786 Building REAL250005074787 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074787' /scratch/stefan/7916156/working/building/REAL250005074787 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074787 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074787/0 /scratch/stefan/7916156/working/building/REAL250005074787 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 908) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/908 `/scratch/stefan/7916156/working/3D/908' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CO)N1C[C@@H]2C[C@@H](CNC(=O)C3=CC(=O)[N-]O3)[C@@H]2C1) `REAL250005074787.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074787/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074787 none O=C(CO)N1C[C@@H]2C[C@@H](CNC(=O)C3=CC(=O)[N-]O3)[C@@H]2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 210 conformations in input total number of sets (complete confs): 210 using faster count positions algorithm for large data unique positions, atoms: [60, 49, 60, 70, 49, 49, 49, 49, 49, 18, 49, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 49, 49, 49, 70, 70, 210, 49, 49, 49, 49, 17, 17, 6, 1, 49, 49] 210 rigid atoms, others: [34, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36]) total number of confs: 453 number of broken/clashed sets: 19 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074787 none O=C(CO)N1C[C@@H]2C[C@@H](CNC(=O)C3=CC(=O)[N-]O3)[C@@H]2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 210 conformations in input total number of sets (complete confs): 210 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 20, 1, 1, 1, 1, 1, 1, 1, 1, 9, 40, 40, 40, 49, 49, 49, 49, 49, 1, 1, 1, 20, 20, 60, 1, 1, 1, 1, 9, 9, 40, 49, 1, 1] 210 rigid atoms, others: [1, 35, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 36, 27, 28, 29, 30] set([0, 32, 2, 3, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 34, 24, 25, 26, 31]) total number of confs: 245 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074787 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074787 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074787/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074787 Building REAL250005074788 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074788' /scratch/stefan/7916156/working/building/REAL250005074788 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074788 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074788/0 /scratch/stefan/7916156/working/building/REAL250005074788 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 909) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/909 `/scratch/stefan/7916156/working/3D/909' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(=O)N1C[C@@H]2C[C@@H](CNC(=O)C3=CC(=O)[N-]O3)[C@@H]2C1) `REAL250005074788.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074788/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074788 none C=CC(=O)N1C[C@@H]2C[C@@H](CNC(=O)C3=CC(=O)[N-]O3)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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, 64, 78, 64, 64, 64, 64, 64, 24, 64, 7, 6, 1, 6, 1, 1, 1, 1, 1, 1, 64, 64, 64, 78, 78, 78, 64, 64, 64, 64, 24, 24, 7, 1, 64, 64] 78 rigid atoms, others: [34, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36]) total number of confs: 240 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074788 none C=CC(=O)N1C[C@@H]2C[C@@H](CNC(=O)C3=CC(=O)[N-]O3)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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: [16, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 64, 64, 64, 64, 64, 1, 1, 1, 16, 16, 16, 1, 1, 1, 1, 10, 10, 50, 64, 1, 1] 78 rigid atoms, others: [2, 35, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 36, 27, 28, 29, 30] set([0, 1, 34, 3, 33, 32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 31]) total number of confs: 189 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074788 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074788 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074788/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074788 Building REAL250005074789 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074789' /scratch/stefan/7916156/working/building/REAL250005074789 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074789 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074789/0 /scratch/stefan/7916156/working/building/REAL250005074789 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 910) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/910 `/scratch/stefan/7916156/working/3D/910' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NC1CCCC12CN(C(=O)C1=CC(=O)[N-]O1)C2) `REAL250005074789.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074789/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074789 none CCC(=O)NC1CCCC12CN(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [46, 38, 38, 38, 24, 25, 25, 25, 25, 25, 25, 8, 1, 8, 1, 1, 1, 1, 1, 1, 24, 46, 46, 46, 46, 46, 38, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 24, 24] 46 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: 140 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074789 none CCC(=O)NC1CCCC12CN(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [23, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 24, 25, 25, 25, 25, 1, 23, 23, 23, 23, 23, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 1, 1] 46 rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 11, 12, 38, 37, 20, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 36, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074789 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074789 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074789/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074789 Building REAL250005074790 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074790' /scratch/stefan/7916156/working/building/REAL250005074790 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074790 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074790/0 /scratch/stefan/7916156/working/building/REAL250005074790 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 911) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/911 `/scratch/stefan/7916156/working/3D/911' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC1CCCC12CN(C(=O)C1=CC(=O)[N-]O1)C2) `REAL250005074790.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074790/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074790 none CC(=O)NC1CCCC12CN(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 11, 11, 11, 11, 11, 11, 11, 6, 1, 6, 1, 1, 1, 1, 1, 1, 10, 12, 12, 12, 12, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 10, 10] 12 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: 26 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074790 none CC(=O)NC1CCCC12CN(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 10, 11, 11, 11, 11, 1, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 1, 1] 12 rigid atoms, others: [32, 35, 34, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 33, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23]) total number of confs: 30 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074790 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074790 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074790/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074790 Building REAL250005074791 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074791' /scratch/stefan/7916156/working/building/REAL250005074791 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074791 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074791/0 /scratch/stefan/7916156/working/building/REAL250005074791 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 912) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/912 `/scratch/stefan/7916156/working/3D/912' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CO)NC1CCCC12CN(C(=O)C1=CC(=O)[N-]O1)C2) `REAL250005074791.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074791/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074791 none O=C(CO)NC1CCCC12CN(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 22, 16, 16, 16, 16, 16, 16, 16, 7, 1, 7, 1, 1, 1, 1, 1, 1, 15, 22, 22, 66, 21, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 15, 15] 66 rigid atoms, others: [34, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36]) total number of confs: 120 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074791 none O=C(CO)NC1CCCC12CN(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 15, 15, 15, 16, 16, 1, 15, 15, 45, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1] 66 rigid atoms, others: [32, 33, 35, 4, 5, 6, 7, 8, 9, 10, 11, 12, 36, 20, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 34, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24]) total number of confs: 124 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074791 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074791 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074791/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074791 Building REAL250005074792 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074792' /scratch/stefan/7916156/working/building/REAL250005074792 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074792 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074792/0 /scratch/stefan/7916156/working/building/REAL250005074792 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 913) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/913 `/scratch/stefan/7916156/working/3D/913' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N1CC2(C1)CCCC2NC(=O)C1=CC(=O)[N-]O1) `REAL250005074792.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074792/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074792 none CCC(=O)N1CC2(C1)CCCC2NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 14, 11, 14, 11, 11, 11, 11, 11, 11, 11, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 8, 1] 19 rigid atoms, others: [38, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 69 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074792 none CCC(=O)N1CC2(C1)CCCC2NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [8, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 11, 11, 11, 11, 11, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 11] 19 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 10, 11, 12, 34, 36, 26, 27, 28, 29, 30, 31] set([0, 1, 3, 37, 38, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074792 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074792 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074792/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074792 Building REAL250005074793 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074793' /scratch/stefan/7916156/working/building/REAL250005074793 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074793 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074793/0 /scratch/stefan/7916156/working/building/REAL250005074793 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 914) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/914 `/scratch/stefan/7916156/working/3D/914' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC2(C1)CCCC2NC(=O)C1=CC(=O)[N-]O1) `REAL250005074793.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074793/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074793 none CC(=O)N1CC2(C1)CCCC2NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 8, 6, 6, 6, 6, 6, 6, 6, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 8, 8, 8, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 1] 8 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: 23 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074793 none CC(=O)N1CC2(C1)CCCC2NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 6, 6, 6, 6, 4, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 6] 8 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 33, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 35, 2, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22]) total number of confs: 21 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074793 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074793 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074793/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074793 Building REAL250005074794 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074794' /scratch/stefan/7916156/working/building/REAL250005074794 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074794 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074794/0 /scratch/stefan/7916156/working/building/REAL250005074794 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 915) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/915 `/scratch/stefan/7916156/working/3D/915' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CO)N1CC2(C1)CCCC2NC(=O)C1=CC(=O)[N-]O1) `REAL250005074794.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074794.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074794/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074794 none O=C(CO)N1CC2(C1)CCCC2NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [16, 12, 16, 20, 12, 12, 12, 12, 12, 12, 12, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 20, 20, 60, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 7, 1] 60 rigid atoms, others: [36, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 129 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074794 none O=C(CO)N1CC2(C1)CCCC2NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 11, 11, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 12] 60 rigid atoms, others: [32, 1, 34, 33, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 35, 2, 3, 36, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23]) total number of confs: 91 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074794 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074794 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074794/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074794 Building REAL250005074795 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074795' /scratch/stefan/7916156/working/building/REAL250005074795 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074795 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074795/0 /scratch/stefan/7916156/working/building/REAL250005074795 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 916) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/916 `/scratch/stefan/7916156/working/3D/916' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(=O)N1CC2(C1)CCCC2NC(=O)C1=CC(=O)[N-]O1) `REAL250005074795.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074795/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074795 none C=CC(=O)N1CC2(C1)CCCC2NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 10, 15, 10, 10, 10, 10, 10, 10, 10, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 15, 15, 15, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 1] 15 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: 41 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074795 none C=CC(=O)N1CC2(C1)CCCC2NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 10, 10, 10, 10, 10, 9, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 10] 15 rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 34, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 3, 36, 35, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074795 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074795 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074795/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074795 Building REAL250005074796 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074796' /scratch/stefan/7916156/working/building/REAL250005074796 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074796 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074796/0 /scratch/stefan/7916156/working/building/REAL250005074796 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 917) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/917 `/scratch/stefan/7916156/working/3D/917' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005074796.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074796/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074796 none CCC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [58, 45, 45, 45, 29, 29, 29, 29, 9, 1, 9, 1, 1, 1, 1, 1, 1, 29, 30, 30, 30, 58, 58, 58, 58, 58, 45, 29, 29, 1, 29, 30, 30, 30, 30] 58 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34]) total number of confs: 188 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074796 none CCC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [28, 5, 5, 5, 1, 1, 1, 1, 1, 1, 6, 6, 29, 30, 30, 30, 29, 1, 1, 1, 1, 28, 28, 28, 28, 28, 5, 1, 1, 29, 1, 1, 2, 2, 2] 58 rigid atoms, others: [4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 27, 28, 30, 31] set([0, 1, 2, 3, 33, 32, 10, 11, 12, 13, 14, 15, 16, 34, 21, 22, 23, 24, 25, 26, 29]) total number of confs: 142 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074796 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074796 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074796/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074796 Building REAL250005074797 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074797' /scratch/stefan/7916156/working/building/REAL250005074797 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074797 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074797/0 /scratch/stefan/7916156/working/building/REAL250005074797 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 918) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/918 `/scratch/stefan/7916156/working/3D/918' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005074797.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074797/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074797 none COCCC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 184 conformations in input total number of sets (complete confs): 184 using faster count positions algorithm for large data unique positions, atoms: [184, 183, 164, 68, 68, 68, 30, 30, 30, 30, 9, 1, 9, 1, 1, 1, 1, 1, 1, 29, 29, 30, 29, 184, 184, 184, 183, 183, 164, 164, 68, 30, 30, 1, 30, 30, 30, 30, 30] 184 rigid atoms, others: [33, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38]) total number of confs: 719 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074797 none COCCC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 184 conformations in input total number of sets (complete confs): 184 using faster count positions algorithm for large data unique positions, atoms: [101, 62, 32, 5, 5, 5, 1, 1, 1, 1, 1, 1, 6, 6, 29, 30, 30, 30, 30, 1, 1, 1, 1, 101, 101, 101, 62, 62, 32, 32, 5, 1, 1, 29, 1, 1, 2, 2, 2] 184 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 33, 36, 37, 38]) total number of confs: 379 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074797 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074797 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074797/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074797 Building REAL250005074798 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074798' /scratch/stefan/7916156/working/building/REAL250005074798 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074798 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074798/0 /scratch/stefan/7916156/working/building/REAL250005074798 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 919) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/919 `/scratch/stefan/7916156/working/3D/919' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005074798.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074798/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074798 none CC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 15, 15, 15, 15, 8, 1, 8, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 18, 18, 18, 18, 15, 15, 1, 15, 15, 15, 15, 15] 18 rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31]) total number of confs: 41 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074798 none CC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 1, 1, 6, 6, 15, 15, 15, 15, 15, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 15, 1, 1, 2, 2, 2] 18 rigid atoms, others: [3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 24, 25, 27, 28] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 26, 29, 30, 31]) total number of confs: 41 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074798 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074798 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074798/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074798 Building REAL250005074799 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074799' /scratch/stefan/7916156/working/building/REAL250005074799 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074799 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074799/0 /scratch/stefan/7916156/working/building/REAL250005074799 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 920) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/920 `/scratch/stefan/7916156/working/3D/920' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C1CC1) `REAL250005074799.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074799/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074799 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 28, 10, 1, 10, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 36, 36, 36, 65, 65, 28, 28, 28, 28, 28, 1, 28, 28, 36, 65, 65, 65, 65, 65] 65 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 27] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 167 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074799 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 28, 28, 28, 28, 28, 1, 1, 1, 1, 5, 5, 5, 32, 32, 2, 2, 2, 1, 1, 28, 1, 1, 5, 32, 32, 32, 32, 32] 65 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 25, 26, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 27, 30, 31, 32, 33, 34, 35]) total number of confs: 120 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.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: REAL250005074799 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 32, 32, 32, 32, 58, 58, 65, 65, 65, 65, 65, 32, 12, 32, 12, 1, 12, 1, 1, 1, 32, 32, 32, 32, 32, 65, 32, 32, 12, 1, 1, 1, 1, 1] 65 rigid atoms, others: [32, 33, 34, 35, 17, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 184 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074799 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074799 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074799/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074799 Building REAL250005074800 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074800' /scratch/stefan/7916156/working/building/REAL250005074800 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074800 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074800/0 /scratch/stefan/7916156/working/building/REAL250005074800 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 921) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/921 `/scratch/stefan/7916156/working/3D/921' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C1CCC1) `REAL250005074800.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074800/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074800 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 26, 9, 1, 9, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 42, 42, 42, 78, 78, 78, 27, 27, 27, 26, 26, 1, 27, 27, 42, 78, 78, 78, 78, 78, 78, 78] 78 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 214 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074800 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 26, 26, 26, 26, 26, 1, 1, 1, 1, 5, 5, 5, 29, 29, 29, 2, 2, 2, 1, 1, 27, 1, 1, 5, 29, 29, 29, 29, 29, 29, 29] 78 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 26, 27, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 113 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.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: REAL250005074800 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 29, 29, 29, 69, 69, 78, 78, 78, 78, 78, 29, 10, 29, 10, 1, 10, 1, 1, 1, 1, 29, 29, 29, 29, 29, 78, 29, 29, 10, 1, 1, 1, 1, 1, 1, 1] 78 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 17, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 209 number of broken/clashed sets: 5 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074800 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074800 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074800/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074800 Building REAL250005074801 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074801' /scratch/stefan/7916156/working/building/REAL250005074801 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074801 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074801/0 /scratch/stefan/7916156/working/building/REAL250005074801 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 922) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/922 `/scratch/stefan/7916156/working/3D/922' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)CC1CC1) `REAL250005074801.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074801/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074801 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)CC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 138 conformations in input total number of sets (complete confs): 138 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 33, 33, 10, 1, 10, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 61, 61, 61, 119, 138, 138, 33, 33, 33, 33, 33, 1, 33, 33, 61, 119, 119, 138, 138, 138, 138, 138] 138 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 506 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074801 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)CC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 138 conformations in input total number of sets (complete confs): 138 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 33, 33, 33, 33, 33, 1, 1, 1, 1, 5, 5, 5, 39, 57, 57, 2, 2, 2, 1, 1, 33, 1, 1, 5, 39, 39, 57, 57, 57, 57, 57] 138 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 26, 27, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 248 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.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: REAL250005074801 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)CC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 138 conformations in input total number of sets (complete confs): 138 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 57, 57, 57, 57, 112, 112, 138, 138, 138, 138, 138, 57, 22, 57, 22, 3, 22, 1, 1, 1, 1, 57, 57, 57, 57, 57, 138, 57, 57, 22, 3, 3, 1, 1, 1, 1, 1] 138 rigid atoms, others: [34, 35, 36, 37, 38, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 381 number of broken/clashed sets: 8 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074801 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074801 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074801/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074801 Building REAL250005074802 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074802' /scratch/stefan/7916156/working/building/REAL250005074802 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074802 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074802/0 /scratch/stefan/7916156/working/building/REAL250005074802 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 923) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/923 `/scratch/stefan/7916156/working/3D/923' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C(C)(C)F) `REAL250005074802.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074802.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074802/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074802 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C(C)(C)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 24, 23, 9, 1, 9, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 43, 43, 43, 70, 70, 70, 24, 24, 24, 23, 23, 1, 24, 24, 43, 70, 70, 70, 70, 70, 70] 70 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 237 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074802 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C(C)(C)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 23, 23, 23, 23, 23, 1, 1, 1, 1, 5, 5, 5, 26, 26, 26, 2, 2, 2, 1, 1, 24, 1, 1, 5, 26, 26, 26, 26, 26, 26] 70 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 26, 27, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 126 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074802 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074802 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074802/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074802 Building REAL250005074803 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074803' /scratch/stefan/7916156/working/building/REAL250005074803 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074803 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074803/0 /scratch/stefan/7916156/working/building/REAL250005074803 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 924) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/924 `/scratch/stefan/7916156/working/3D/924' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005074803.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074803/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074803 none COCC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [88, 88, 53, 53, 53, 26, 26, 26, 26, 9, 1, 9, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 88, 88, 88, 88, 88, 53, 26, 26, 1, 26, 26, 26, 26, 26] 88 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 304 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074803 none COCC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [46, 33, 5, 5, 5, 1, 1, 1, 1, 1, 1, 6, 6, 26, 26, 26, 26, 26, 1, 1, 1, 1, 46, 46, 46, 33, 33, 5, 1, 1, 26, 1, 1, 2, 2, 2] 88 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 28, 29, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 30, 33, 34, 35]) total number of confs: 174 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074803 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074803 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074803/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074803 Building REAL250005074804 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074804' /scratch/stefan/7916156/working/building/REAL250005074804 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074804 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074804/0 /scratch/stefan/7916156/working/building/REAL250005074804 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 925) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/925 `/scratch/stefan/7916156/working/3D/925' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005074804.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074804/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074804 none CCCC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [109, 108, 63, 63, 63, 33, 33, 33, 33, 9, 1, 9, 1, 1, 1, 1, 1, 1, 32, 32, 33, 33, 109, 109, 109, 109, 109, 108, 108, 63, 33, 33, 1, 33, 33, 33, 33, 33] 109 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37]) total number of confs: 384 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074804 none CCCC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [38, 29, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 33, 33, 33, 33, 33, 1, 1, 1, 1, 44, 44, 44, 44, 44, 29, 29, 5, 1, 1, 32, 1, 1, 2, 2, 2] 109 rigid atoms, others: [33, 34, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 32, 35, 36, 37]) total number of confs: 272 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074804 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074804 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074804/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074804 Building REAL250005074805 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074805' /scratch/stefan/7916156/working/building/REAL250005074805 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074805 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074805/0 /scratch/stefan/7916156/working/building/REAL250005074805 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 926) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/926 `/scratch/stefan/7916156/working/3D/926' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005074805.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074805/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074805 none CC(C)CC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [62, 64, 64, 40, 40, 40, 24, 24, 24, 24, 8, 1, 8, 1, 1, 1, 1, 1, 1, 23, 23, 24, 24, 64, 64, 64, 64, 64, 64, 64, 64, 64, 40, 24, 24, 1, 24, 24, 24, 24, 24] 64 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: 248 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074805 none CC(C)CC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [15, 16, 18, 5, 5, 5, 1, 1, 1, 1, 1, 1, 6, 7, 23, 24, 24, 24, 24, 1, 1, 1, 1, 18, 18, 18, 18, 18, 18, 18, 16, 16, 5, 1, 1, 23, 1, 1, 2, 2, 2] 64 rigid atoms, others: [33, 34, 36, 37, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 38, 39, 40]) total number of confs: 128 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074805 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074805 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074805/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074805 Building REAL250005074806 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074806' /scratch/stefan/7916156/working/building/REAL250005074806 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074806 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074806/0 /scratch/stefan/7916156/working/building/REAL250005074806 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 927) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/927 `/scratch/stefan/7916156/working/3D/927' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC1C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005074806.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074806/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074806 none CC1CC1C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 20, 5, 5, 5, 1, 1, 1, 1, 1, 1, 6, 6, 22, 22, 22, 22, 22, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 5, 1, 1, 22, 1, 1, 2, 2, 2] 67 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 33, 36, 37, 38]) total number of confs: 89 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074806 none CC1CC1C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 9, 9, 9, 20, 20, 20, 20, 49, 49, 67, 67, 67, 67, 67, 20, 20, 20, 20, 2, 2, 2, 1, 1, 1, 1, 9, 20, 20, 67, 20, 20, 20, 20, 20] 67 rigid atoms, others: [0, 1, 2, 3, 4, 26, 27, 28, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 179 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.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: REAL250005074806 none CC1CC1C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 67, 44, 44, 44, 22, 22, 22, 22, 10, 1, 10, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 67, 67, 67, 67, 67, 67, 67, 44, 22, 22, 1, 22, 22, 22, 22, 22] 67 rigid atoms, others: [33, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38]) total number of confs: 202 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074806 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074806 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074806/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074806 Building REAL250005074807 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074807' /scratch/stefan/7916156/working/building/REAL250005074807 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074807 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074807/0 /scratch/stefan/7916156/working/building/REAL250005074807 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 928) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/928 `/scratch/stefan/7916156/working/3D/928' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005074807.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074807/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074807 none CCOCC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 148 conformations in input total number of sets (complete confs): 148 using faster count positions algorithm for large data unique positions, atoms: [148, 148, 137, 64, 64, 64, 27, 27, 27, 26, 9, 1, 9, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 148, 148, 148, 148, 148, 137, 137, 64, 26, 26, 1, 27, 27, 27, 27, 27] 148 rigid atoms, others: [33, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38]) total number of confs: 510 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074807 none CCOCC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 148 conformations in input total number of sets (complete confs): 148 using faster count positions algorithm for large data unique positions, atoms: [91, 84, 38, 5, 5, 5, 1, 1, 1, 1, 1, 1, 6, 6, 27, 27, 27, 26, 26, 1, 1, 1, 1, 91, 91, 91, 91, 91, 38, 38, 5, 1, 1, 27, 1, 1, 2, 2, 2] 148 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 33, 36, 37, 38]) total number of confs: 281 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074807 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074807 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074807/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074807 Building REAL250005074808 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074808' /scratch/stefan/7916156/working/building/REAL250005074808 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074808 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074808/0 /scratch/stefan/7916156/working/building/REAL250005074808 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 929) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/929 `/scratch/stefan/7916156/working/3D/929' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)=CC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005074808.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074808/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074808 none CC(C)=CC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 48, 48, 48, 27, 27, 27, 27, 9, 1, 9, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 63, 63, 63, 63, 63, 63, 63, 48, 27, 27, 1, 27, 27, 27, 27, 27] 63 rigid atoms, others: [33, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38]) total number of confs: 174 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074808 none CC(C)=CC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 15, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 27, 27, 27, 27, 27, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 5, 1, 1, 27, 1, 1, 2, 2, 2] 63 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 33, 36, 37, 38]) total number of confs: 85 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074808 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074808 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074808/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074808 Building REAL250005074809 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074809' /scratch/stefan/7916156/working/building/REAL250005074809 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074809 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074809/0 /scratch/stefan/7916156/working/building/REAL250005074809 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 930) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/930 `/scratch/stefan/7916156/working/3D/930' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSCC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005074809.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074809/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074809 none CSCC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [151, 138, 64, 64, 64, 29, 29, 29, 29, 10, 1, 10, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 151, 151, 151, 138, 138, 64, 29, 29, 1, 29, 29, 29, 29, 29] 151 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 516 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074809 none CSCC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [83, 35, 5, 5, 5, 1, 1, 1, 1, 1, 1, 6, 6, 29, 29, 29, 29, 29, 1, 1, 1, 1, 81, 83, 83, 35, 35, 5, 1, 1, 29, 1, 1, 2, 2, 2] 151 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 28, 29, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 30, 33, 34, 35]) total number of confs: 235 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074809 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074809 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074809/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074809 Building REAL250005074810 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074810' /scratch/stefan/7916156/working/building/REAL250005074810 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074810 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074810/0 /scratch/stefan/7916156/working/building/REAL250005074810 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 931) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/931 `/scratch/stefan/7916156/working/3D/931' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005074810.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074810/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074810 none CCCCC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 198 conformations in input total number of sets (complete confs): 198 using faster count positions algorithm for large data unique positions, atoms: [196, 193, 172, 69, 69, 69, 30, 30, 30, 30, 9, 1, 9, 1, 1, 1, 1, 1, 1, 29, 29, 30, 30, 196, 198, 198, 198, 198, 194, 194, 172, 172, 69, 30, 30, 1, 30, 30, 30, 30, 30] 198 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: 816 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074810 none CCCCC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 198 conformations in input total number of sets (complete confs): 198 using faster count positions algorithm for large data unique positions, atoms: [88, 48, 33, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 30, 30, 30, 30, 30, 1, 1, 1, 1, 88, 94, 94, 88, 91, 57, 57, 33, 33, 5, 1, 1, 29, 1, 1, 2, 2, 2] 198 rigid atoms, others: [33, 34, 36, 37, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 38, 39, 40]) total number of confs: 518 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074810 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074810 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074810/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074810 Building REAL250005074811 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074811' /scratch/stefan/7916156/working/building/REAL250005074811 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074811 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074811/0 /scratch/stefan/7916156/working/building/REAL250005074811 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 932) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/932 `/scratch/stefan/7916156/working/3D/932' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005074811.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074811/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074811 none CC(C)C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [68, 52, 68, 52, 52, 35, 35, 35, 35, 9, 1, 9, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 68, 68, 68, 68, 68, 68, 68, 52, 35, 35, 1, 35, 35, 35, 35, 35] 68 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37]) total number of confs: 207 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074811 none CC(C)C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [24, 5, 24, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 35, 35, 35, 35, 35, 1, 1, 1, 1, 24, 24, 24, 24, 24, 24, 24, 5, 1, 1, 35, 1, 1, 2, 2, 2] 68 rigid atoms, others: [33, 34, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 32, 35, 36, 37]) total number of confs: 134 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074811 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074811 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074811/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074811 Building REAL250005074812 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074812' /scratch/stefan/7916156/working/building/REAL250005074812 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074812 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074812/0 /scratch/stefan/7916156/working/building/REAL250005074812 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 933) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/933 `/scratch/stefan/7916156/working/3D/933' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005074812.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074812/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074812 none CCC(C)C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 106 conformations in input total number of sets (complete confs): 106 using faster count positions algorithm for large data unique positions, atoms: [106, 105, 59, 105, 59, 59, 30, 30, 30, 30, 10, 1, 10, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 106, 106, 106, 106, 106, 105, 105, 105, 105, 59, 30, 30, 1, 30, 30, 30, 30, 30] 106 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: 363 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074812 none CCC(C)C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 106 conformations in input total number of sets (complete confs): 106 using faster count positions algorithm for large data unique positions, atoms: [38, 30, 5, 30, 5, 5, 1, 1, 1, 1, 1, 1, 6, 6, 30, 30, 30, 30, 30, 1, 1, 1, 1, 42, 42, 42, 42, 42, 30, 30, 30, 30, 5, 1, 1, 30, 1, 1, 2, 2, 2] 106 rigid atoms, others: [33, 34, 36, 37, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 38, 39, 40]) total number of confs: 241 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074812 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074812 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074812/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074812 Building REAL250005074813 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074813' /scratch/stefan/7916156/working/building/REAL250005074813 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074813 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074813/0 /scratch/stefan/7916156/working/building/REAL250005074813 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 934) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/934 `/scratch/stefan/7916156/working/3D/934' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005074813.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074813/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074813 none COC(C)C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [61, 61, 42, 61, 42, 42, 25, 25, 25, 25, 9, 1, 9, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 61, 61, 61, 61, 61, 61, 61, 42, 25, 25, 1, 25, 25, 25, 25, 25] 61 rigid atoms, others: [33, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38]) total number of confs: 200 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074813 none COC(C)C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [28, 21, 5, 21, 5, 5, 1, 1, 1, 1, 1, 1, 6, 6, 25, 25, 25, 25, 25, 1, 1, 1, 1, 28, 28, 28, 21, 21, 21, 21, 5, 1, 1, 25, 1, 1, 2, 2, 2] 61 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 33, 36, 37, 38]) total number of confs: 125 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074813 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074813 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074813/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074813 Building REAL250005074814 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074814' /scratch/stefan/7916156/working/building/REAL250005074814 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074814 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074814/0 /scratch/stefan/7916156/working/building/REAL250005074814 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 935) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/935 `/scratch/stefan/7916156/working/3D/935' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005074814.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074814/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074814 none C=CCCC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 173, 65, 65, 65, 27, 27, 27, 27, 9, 1, 9, 1, 1, 1, 1, 1, 1, 26, 26, 27, 26, 201, 201, 201, 201, 201, 173, 173, 65, 27, 27, 1, 27, 27, 27, 27, 27] 201 rigid atoms, others: [33, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38]) total number of confs: 796 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074814 none C=CCCC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [119, 64, 35, 5, 5, 5, 1, 1, 1, 1, 1, 1, 6, 6, 26, 27, 27, 27, 27, 1, 1, 1, 1, 119, 119, 119, 64, 64, 35, 35, 5, 1, 1, 26, 1, 1, 2, 2, 2] 201 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 33, 36, 37, 38]) total number of confs: 498 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074814 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074814 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074814/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074814 Building REAL250005074815 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074815' /scratch/stefan/7916156/working/building/REAL250005074815 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074815 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074815/0 /scratch/stefan/7916156/working/building/REAL250005074815 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 936) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/936 `/scratch/stefan/7916156/working/3D/936' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=C(C)C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005074815.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074815/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074815 none CC=C(C)C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [64, 64, 37, 64, 37, 37, 26, 26, 26, 26, 9, 1, 9, 1, 1, 1, 1, 1, 1, 25, 25, 26, 26, 64, 64, 64, 64, 64, 64, 64, 37, 26, 26, 1, 26, 26, 26, 26, 26] 64 rigid atoms, others: [33, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38]) total number of confs: 178 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074815 none CC=C(C)C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 5, 27, 5, 5, 1, 1, 1, 1, 1, 1, 6, 6, 25, 26, 26, 26, 26, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 27, 5, 1, 1, 25, 1, 1, 2, 2, 2] 64 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 33, 36, 37, 38]) total number of confs: 108 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074815 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074815 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074815/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074815 Building REAL250005074816 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074816' /scratch/stefan/7916156/working/building/REAL250005074816 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074816 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074816/0 /scratch/stefan/7916156/working/building/REAL250005074816 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 937) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/937 `/scratch/stefan/7916156/working/3D/937' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C1(C)CC1) `REAL250005074816.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074816/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074816 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C1(C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 19, 9, 1, 9, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 25, 25, 25, 82, 82, 82, 19, 19, 19, 19, 19, 1, 19, 19, 25, 82, 82, 82, 82, 82, 82, 82] 82 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 215 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074816 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C1(C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 19, 19, 19, 19, 19, 1, 1, 1, 1, 4, 4, 4, 19, 19, 19, 2, 2, 2, 1, 1, 19, 1, 1, 4, 19, 19, 19, 19, 19, 19, 19] 82 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 26, 27, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 81 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.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: REAL250005074816 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C1(C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 19, 19, 19, 68, 68, 82, 82, 82, 82, 82, 19, 6, 19, 6, 1, 6, 1, 1, 1, 1, 19, 19, 19, 19, 19, 82, 19, 19, 6, 2, 2, 2, 1, 1, 1, 1] 82 rigid atoms, others: [35, 36, 37, 38, 17, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 213 number of broken/clashed sets: 7 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074816 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074816 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074816/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074816 Building REAL250005074817 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074817' /scratch/stefan/7916156/working/building/REAL250005074817 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074817 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074817/0 /scratch/stefan/7916156/working/building/REAL250005074817 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 938) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/938 `/scratch/stefan/7916156/working/3D/938' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H]1C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005074817.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074817/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074817 none C[C@@H]1C[C@H]1C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 32, 32, 5, 32, 5, 5, 1, 1, 1, 1, 1, 1, 6, 6, 27, 28, 28, 28, 28, 1, 1, 1, 1, 32, 32, 32, 32, 32, 5, 1, 1, 27, 1, 1, 2, 2, 2] 78 rigid atoms, others: [32, 34, 35, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 33, 36, 37, 38]) total number of confs: 120 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074817 none C[C@@H]1C[C@H]1C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 13, 13, 13, 32, 32, 32, 32, 67, 67, 78, 78, 78, 78, 78, 32, 32, 32, 32, 2, 2, 2, 1, 1, 13, 32, 32, 78, 32, 32, 32, 32, 32] 78 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 218 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.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: REAL250005074817 none C[C@@H]1C[C@H]1C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 46, 78, 46, 46, 27, 27, 27, 27, 9, 1, 9, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 78, 78, 78, 78, 78, 46, 27, 27, 1, 27, 27, 28, 28, 28] 78 rigid atoms, others: [33, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38]) total number of confs: 223 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074817 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074817 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074817/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074817 Building REAL250005074818 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074818' /scratch/stefan/7916156/working/building/REAL250005074818 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074818 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074818/0 /scratch/stefan/7916156/working/building/REAL250005074818 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 939) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/939 `/scratch/stefan/7916156/working/3D/939' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(F)C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005074818.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074818/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074818 none CCC(F)C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [121, 120, 63, 120, 63, 63, 30, 30, 30, 30, 9, 1, 9, 1, 1, 1, 1, 1, 1, 29, 29, 30, 29, 121, 121, 121, 121, 121, 120, 63, 30, 30, 1, 29, 29, 30, 30, 30] 121 rigid atoms, others: [32, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37]) total number of confs: 432 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074818 none CCC(F)C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [47, 34, 5, 34, 5, 5, 1, 1, 1, 1, 1, 1, 6, 6, 29, 29, 29, 30, 30, 1, 1, 1, 1, 55, 55, 55, 55, 55, 34, 5, 1, 1, 29, 1, 1, 2, 2, 2] 121 rigid atoms, others: [33, 34, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 32, 35, 36, 37]) total number of confs: 318 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074818 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074818 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074818/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074818 Building REAL250005074819 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074819' /scratch/stefan/7916156/working/building/REAL250005074819 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074819 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074819/0 /scratch/stefan/7916156/working/building/REAL250005074819 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 940) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/940 `/scratch/stefan/7916156/working/3D/940' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)CCCF) `REAL250005074819.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074819/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074819 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)CCCF NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 184 conformations in input total number of sets (complete confs): 184 using faster count positions algorithm for large data unique positions, atoms: [24, 25, 25, 24, 6, 1, 6, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 63, 63, 63, 166, 169, 184, 25, 25, 25, 25, 25, 1, 25, 25, 63, 166, 166, 184, 184, 184, 184] 184 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 802 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074819 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)CCCF NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 184 conformations in input total number of sets (complete confs): 184 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 24, 25, 25, 25, 25, 1, 1, 1, 1, 5, 5, 5, 30, 45, 100, 2, 2, 2, 1, 1, 24, 1, 1, 5, 30, 30, 58, 58, 98, 96] 184 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 26, 27, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 530 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074819 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074819 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074819/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074819 Building REAL250005074820 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074820' /scratch/stefan/7916156/working/building/REAL250005074820 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074820 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074820/0 /scratch/stefan/7916156/working/building/REAL250005074820 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 941) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/941 `/scratch/stefan/7916156/working/3D/941' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@@H]1C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005074820.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074820/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074820 none C[C@H]1C[C@@H]1C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 36, 36, 5, 36, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 30, 30, 30, 30, 30, 1, 1, 1, 1, 36, 36, 36, 36, 36, 5, 1, 1, 30, 1, 1, 2, 2, 2] 97 rigid atoms, others: [32, 34, 35, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 33, 36, 37, 38]) total number of confs: 130 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074820 none C[C@H]1C[C@@H]1C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 36, 36, 36, 36, 84, 84, 97, 97, 97, 97, 97, 36, 36, 36, 36, 2, 2, 2, 1, 1, 12, 36, 36, 97, 36, 36, 36, 36, 36] 97 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 262 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.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: REAL250005074820 none C[C@H]1C[C@@H]1C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 58, 97, 58, 58, 30, 30, 30, 30, 9, 1, 9, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 97, 97, 97, 97, 97, 58, 30, 30, 1, 30, 30, 30, 30, 30] 97 rigid atoms, others: [33, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38]) total number of confs: 278 number of broken/clashed sets: 5 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074820 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074820 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074820/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074820 Building REAL250005074821 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074821' /scratch/stefan/7916156/working/building/REAL250005074821 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074821 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074821/0 /scratch/stefan/7916156/working/building/REAL250005074821 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 942) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/942 `/scratch/stefan/7916156/working/3D/942' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C(N)=O) `REAL250005074821.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074821/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074821 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 10, 1, 10, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 39, 39, 39, 50, 50, 23, 23, 23, 23, 23, 1, 23, 23, 39, 50, 50] 50 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 27] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32]) total number of confs: 135 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074821 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 23, 23, 23, 23, 23, 1, 1, 1, 1, 5, 5, 5, 18, 18, 2, 2, 2, 1, 1, 23, 1, 1, 5, 18, 18] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 25, 26, 28, 29] set([32, 6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 27, 30, 31]) total number of confs: 85 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074821 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074821 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074821/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074821 Building REAL250005074822 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074822' /scratch/stefan/7916156/working/building/REAL250005074822 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074822 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074822/0 /scratch/stefan/7916156/working/building/REAL250005074822 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 943) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/943 `/scratch/stefan/7916156/working/3D/943' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C(C)(C)C) `REAL250005074822.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074822/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074822 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [20, 21, 21, 20, 8, 1, 8, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 29, 29, 29, 32, 32, 32, 21, 21, 21, 21, 21, 1, 21, 21, 29, 32, 32, 32, 32, 32, 32, 32, 32, 32] 32 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 98 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074822 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 20, 21, 21, 21, 21, 1, 1, 1, 1, 5, 5, 5, 8, 8, 8, 2, 2, 2, 1, 1, 20, 1, 1, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8] 32 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 26, 27, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 69 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074822 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074822 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074822/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074822 Building REAL250005074823 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074823' /scratch/stefan/7916156/working/building/REAL250005074823 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074823 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074823/0 /scratch/stefan/7916156/working/building/REAL250005074823 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 944) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/944 `/scratch/stefan/7916156/working/3D/944' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005074823.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074823/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074823 none C=CCC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [88, 88, 53, 53, 53, 29, 29, 29, 29, 10, 1, 10, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 88, 88, 88, 88, 88, 53, 29, 29, 1, 29, 29, 29, 29, 29] 88 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 310 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074823 none C=CCC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [49, 31, 5, 5, 5, 1, 1, 1, 1, 1, 1, 6, 7, 29, 29, 29, 29, 29, 1, 1, 1, 1, 49, 49, 49, 31, 31, 5, 1, 1, 29, 1, 1, 2, 2, 2] 88 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 28, 29, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 30, 33, 34, 35]) total number of confs: 212 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074823 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074823 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074823/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074823 Building REAL250005074824 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074824' /scratch/stefan/7916156/working/building/REAL250005074824 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005074824 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074824/0 /scratch/stefan/7916156/working/building/REAL250005074824 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 945) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/945 `/scratch/stefan/7916156/working/3D/945' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C[NH+](C)C) `REAL250005074824.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074824/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074824 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 8, 8, 8, 8, 8, 8, 8, 6, 6, 6, 5, 5, 1, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8] 8 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 19 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074824 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 2, 5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 4, 4, 5, 6, 6, 6, 2, 2, 2, 1, 1, 5, 1, 1, 4, 5, 5, 6, 6, 6, 6, 6, 6] 8 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 27, 28, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 36 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074824 /scratch/stefan/7916156/working /scratch/stefan/7916156 mkdir: created directory `1' /scratch/stefan/7916156/working/building/REAL250005074824/1 /scratch/stefan/7916156/working/building/REAL250005074824 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 1 (index: 946) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/946 `/scratch/stefan/7916156/working/3D/946' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)CN(C)C) `REAL250005074824.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005074824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074824/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074824 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)CN(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 21, 9, 1, 9, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 42, 42, 42, 77, 77, 77, 22, 22, 22, 21, 21, 1, 22, 22, 42, 77, 77, 77, 77, 77, 77, 77, 77] 77 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 275 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074824 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)CN(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 21, 21, 21, 21, 21, 1, 1, 1, 1, 4, 4, 4, 26, 29, 29, 2, 2, 2, 1, 1, 22, 1, 1, 4, 26, 26, 29, 29, 29, 29, 29, 29] 77 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 26, 27, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074824 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074824 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 1: /scratch/stefan/7916156/working/building/REAL250005074824/1.* 0: /scratch/stefan/7916156/working/building/REAL250005074824/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074824 Building REAL250005074825 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074825' /scratch/stefan/7916156/working/building/REAL250005074825 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074825 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074825/0 /scratch/stefan/7916156/working/building/REAL250005074825 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 947) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/947 `/scratch/stefan/7916156/working/3D/947' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(O)C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005074825.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074825/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074825 none C=CC(O)C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 258 conformations in input total number of sets (complete confs): 258 using faster count positions algorithm for large data unique positions, atoms: [86, 86, 56, 86, 56, 56, 26, 26, 26, 26, 9, 1, 9, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 86, 86, 86, 86, 258, 56, 26, 26, 1, 26, 26, 26, 26, 26] 258 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36]) total number of confs: 547 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074825 none C=CC(O)C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 258 conformations in input total number of sets (complete confs): 258 using faster count positions algorithm for large data unique positions, atoms: [55, 30, 5, 30, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 26, 26, 26, 26, 26, 1, 1, 1, 1, 55, 55, 55, 30, 90, 5, 1, 1, 26, 1, 1, 2, 2, 2] 258 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 31, 34, 35, 36]) total number of confs: 313 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074825 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074825 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074825/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074825 Building REAL250005074826 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074826' /scratch/stefan/7916156/working/building/REAL250005074826 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074826 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074826/0 /scratch/stefan/7916156/working/building/REAL250005074826 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 948) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/948 `/scratch/stefan/7916156/working/3D/948' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C1COC1) `REAL250005074826.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074826/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074826 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C1COC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 28, 9, 1, 9, 1, 1, 1, 1, 1, 1, 28, 29, 29, 29, 53, 53, 53, 80, 80, 80, 29, 29, 29, 28, 28, 1, 28, 28, 53, 80, 80, 80, 80, 80] 80 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 215 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074826 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C1COC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 28, 28, 29, 28, 28, 1, 1, 1, 1, 5, 5, 5, 29, 29, 29, 2, 2, 2, 1, 1, 28, 1, 1, 5, 29, 29, 29, 29, 29] 80 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 26, 27, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 31, 32, 33, 34, 35, 36]) total number of confs: 115 number of broken/clashed sets: 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.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: REAL250005074826 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C1COC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 29, 29, 29, 68, 68, 80, 80, 80, 80, 80, 29, 10, 29, 10, 1, 10, 1, 1, 1, 1, 29, 29, 29, 29, 29, 80, 29, 29, 10, 1, 1, 1, 1, 1] 80 rigid atoms, others: [32, 33, 34, 35, 36, 17, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 217 number of broken/clashed sets: 8 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074826 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074826 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074826/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074826 Building REAL250005074827 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074827' /scratch/stefan/7916156/working/building/REAL250005074827 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074827 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074827/0 /scratch/stefan/7916156/working/building/REAL250005074827 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 949) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/949 `/scratch/stefan/7916156/working/3D/949' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](C)C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005074827.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074827/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074827 none CO[C@H](C)C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 42, 57, 57, 42, 42, 22, 22, 22, 22, 10, 1, 10, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 57, 57, 57, 57, 57, 57, 42, 22, 22, 1, 22, 22, 22, 22, 22] 57 rigid atoms, others: [33, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38]) total number of confs: 183 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074827 none CO[C@H](C)C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [29, 23, 5, 23, 23, 5, 5, 1, 1, 1, 1, 1, 1, 6, 6, 22, 22, 22, 22, 22, 1, 1, 1, 1, 29, 29, 29, 23, 23, 23, 5, 1, 1, 22, 1, 1, 2, 2, 2] 57 rigid atoms, others: [32, 34, 35, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 33, 36, 37, 38]) total number of confs: 125 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074827 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074827 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074827/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074827 Building REAL250005074828 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074828' /scratch/stefan/7916156/working/building/REAL250005074828 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074828 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074828/0 /scratch/stefan/7916156/working/building/REAL250005074828 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 950) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/950 `/scratch/stefan/7916156/working/3D/950' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC=CC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005074828.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074828.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074828/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074828 none CCC=CC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 110 conformations in input total number of sets (complete confs): 110 using faster count positions algorithm for large data unique positions, atoms: [110, 91, 91, 58, 58, 58, 29, 29, 29, 29, 9, 1, 9, 1, 1, 1, 1, 1, 1, 28, 28, 29, 29, 110, 110, 110, 110, 110, 91, 91, 58, 29, 29, 1, 29, 29, 29, 29, 29] 110 rigid atoms, others: [33, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38]) total number of confs: 389 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074828 none CCC=CC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 110 conformations in input total number of sets (complete confs): 110 using faster count positions algorithm for large data unique positions, atoms: [51, 30, 30, 5, 5, 5, 1, 1, 1, 1, 1, 1, 6, 6, 28, 29, 29, 29, 29, 1, 1, 1, 1, 51, 51, 51, 51, 51, 30, 30, 5, 1, 1, 28, 1, 1, 2, 2, 2] 110 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 33, 36, 37, 38]) total number of confs: 234 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074828 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074828 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074828/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074828 Building REAL250005074829 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074829' /scratch/stefan/7916156/working/building/REAL250005074829 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074829 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074829/0 /scratch/stefan/7916156/working/building/REAL250005074829 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 951) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/951 `/scratch/stefan/7916156/working/3D/951' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)CN=[N+]=[N-]) `REAL250005074829.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074829/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074829 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)CN=[N+]=[N-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.2', 'N.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 30, 30, 10, 1, 10, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 62, 62, 62, 182, 201, 201, 30, 30, 30, 30, 30, 1, 30, 30, 62, 182, 182] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33]) total number of confs: 679 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074829 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)CN=[N+]=[N-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.2', 'N.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 30, 30, 30, 30, 30, 1, 1, 1, 1, 5, 5, 5, 43, 132, 132, 2, 2, 2, 1, 1, 30, 1, 1, 5, 43, 43] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 26, 27, 29, 30] set([32, 33, 6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 31]) total number of confs: 307 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074829 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074829 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074829/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074829 Building REAL250005074830 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074830' /scratch/stefan/7916156/working/building/REAL250005074830 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074830 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074830/0 /scratch/stefan/7916156/working/building/REAL250005074830 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 952) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/952 `/scratch/stefan/7916156/working/3D/952' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)CO) `REAL250005074830.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074830/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074830 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 25, 25, 10, 1, 10, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 32, 32, 32, 34, 25, 25, 25, 25, 25, 1, 25, 25, 32, 34, 34, 102] 102 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 26] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32]) total number of confs: 181 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074830 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 25, 25, 25, 25, 25, 1, 1, 1, 1, 4, 4, 4, 19, 2, 2, 2, 1, 1, 25, 1, 1, 4, 19, 19, 57] 102 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 24, 25, 27, 28] set([32, 6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 26, 29, 30, 31]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074830 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074830 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074830/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074830 Building REAL250005074831 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074831' /scratch/stefan/7916156/working/building/REAL250005074831 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074831 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074831/0 /scratch/stefan/7916156/working/building/REAL250005074831 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 953) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/953 `/scratch/stefan/7916156/working/3D/953' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005074831.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074831.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074831/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074831 none CC(O)C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [49, 38, 49, 38, 38, 23, 23, 23, 23, 9, 1, 9, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 49, 49, 49, 49, 147, 38, 23, 23, 1, 23, 23, 23, 23, 23] 147 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 296 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074831 none CC(O)C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [29, 5, 29, 5, 5, 1, 1, 1, 1, 1, 1, 6, 6, 23, 23, 23, 23, 23, 1, 1, 1, 1, 29, 29, 29, 29, 87, 5, 1, 1, 23, 1, 1, 2, 2, 2] 147 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 28, 29, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 30, 33, 34, 35]) total number of confs: 222 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074831 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074831 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074831/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074831 Building REAL250005074832 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074832' /scratch/stefan/7916156/working/building/REAL250005074832 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074832 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074832/0 /scratch/stefan/7916156/working/building/REAL250005074832 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 954) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/954 `/scratch/stefan/7916156/working/3D/954' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C1CC1F) `REAL250005074832.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074832/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074832 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C1CC1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 28, 9, 1, 9, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 61, 61, 61, 96, 96, 96, 28, 28, 28, 28, 28, 1, 28, 28, 61, 96, 96, 96, 96] 96 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 270 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074832 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C1CC1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 7, 7, 28, 28, 28, 28, 28, 1, 1, 1, 1, 5, 5, 5, 36, 36, 36, 2, 2, 2, 1, 1, 28, 1, 1, 5, 36, 36, 36, 36] 96 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 26, 27, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 31, 32, 33, 34, 35]) total number of confs: 128 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.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: REAL250005074832 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C1CC1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 36, 36, 36, 36, 85, 85, 96, 96, 96, 96, 96, 36, 13, 36, 13, 1, 13, 1, 1, 1, 1, 36, 36, 36, 36, 36, 96, 36, 36, 13, 1, 1, 1, 1] 96 rigid atoms, others: [32, 33, 34, 35, 17, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 261 number of broken/clashed sets: 5 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074832 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074832 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074832/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074832 Building REAL250005074833 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074833' /scratch/stefan/7916156/working/building/REAL250005074833 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074833 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074833/0 /scratch/stefan/7916156/working/building/REAL250005074833 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 955) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/955 `/scratch/stefan/7916156/working/3D/955' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)CCF) `REAL250005074833.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074833.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074833/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074833 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)CCF NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 26, 8, 1, 8, 1, 1, 1, 1, 1, 1, 26, 27, 27, 27, 52, 52, 52, 108, 108, 27, 27, 27, 26, 26, 1, 27, 27, 52, 108, 108, 108, 108] 108 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 27] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 390 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074833 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)CCF NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 26, 26, 26, 26, 26, 1, 1, 1, 1, 5, 5, 5, 31, 54, 2, 2, 2, 1, 1, 26, 1, 1, 5, 31, 31, 54, 54] 108 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 25, 26, 28, 29] set([32, 33, 34, 6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 27, 30, 31]) total number of confs: 268 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074833 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074833 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074833/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074833 Building REAL250005074834 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074834' /scratch/stefan/7916156/working/building/REAL250005074834 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074834 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074834/0 /scratch/stefan/7916156/working/building/REAL250005074834 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 956) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/956 `/scratch/stefan/7916156/working/3D/956' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C=CCF) `REAL250005074834.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074834/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074834 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C=CCF NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 1, 1, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 26, 25, 9, 1, 9, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 46, 46, 46, 75, 75, 81, 26, 26, 26, 25, 25, 1, 26, 26, 46, 75, 75, 81, 81] 81 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 250 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074834 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C=CCF NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 1, 1, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 25, 25, 25, 26, 26, 1, 1, 1, 1, 5, 5, 5, 21, 21, 49, 2, 2, 2, 1, 1, 25, 1, 1, 5, 21, 21, 49, 49] 81 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 26, 27, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 31, 32, 33, 34, 35]) total number of confs: 212 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074834 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074834 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074834/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074834 Building REAL250005074835 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074835' /scratch/stefan/7916156/working/building/REAL250005074835 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074835 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074835/0 /scratch/stefan/7916156/working/building/REAL250005074835 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 957) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/957 `/scratch/stefan/7916156/working/3D/957' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005074835.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074835/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074835 none C#CCCC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 134 conformations in input total number of sets (complete confs): 134 using faster count positions algorithm for large data unique positions, atoms: [134, 134, 125, 64, 64, 64, 30, 30, 30, 30, 8, 1, 8, 1, 1, 1, 1, 1, 1, 29, 29, 30, 29, 134, 134, 134, 125, 125, 64, 30, 30, 1, 30, 30, 30, 30, 30] 134 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36]) total number of confs: 505 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074835 none C#CCCC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 134 conformations in input total number of sets (complete confs): 134 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 30, 5, 5, 5, 1, 1, 1, 1, 1, 1, 6, 6, 29, 30, 30, 30, 30, 1, 1, 1, 1, 56, 56, 56, 30, 30, 5, 1, 1, 29, 1, 1, 2, 2, 2] 134 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 31, 34, 35, 36]) total number of confs: 285 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074835 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074835 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074835/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074835 Building REAL250005074836 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074836' /scratch/stefan/7916156/working/building/REAL250005074836 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074836 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074836/0 /scratch/stefan/7916156/working/building/REAL250005074836 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 958) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/958 `/scratch/stefan/7916156/working/3D/958' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C1CCO1) `REAL250005074836.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074836.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074836/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074836 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C1CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 10, 1, 10, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 34, 34, 34, 44, 44, 44, 23, 23, 23, 23, 23, 1, 23, 23, 34, 44, 44, 44, 44, 44] 44 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 117 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074836 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C1CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 23, 23, 23, 23, 23, 1, 1, 1, 1, 5, 5, 5, 25, 25, 25, 2, 2, 2, 1, 1, 23, 1, 1, 5, 25, 25, 25, 25, 25] 44 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 26, 27, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 31, 32, 33, 34, 35, 36]) total number of confs: 99 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.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: REAL250005074836 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C1CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 25, 25, 41, 41, 44, 44, 44, 44, 44, 25, 10, 25, 10, 1, 10, 1, 1, 1, 1, 25, 25, 25, 25, 25, 44, 25, 25, 10, 1, 1, 1, 1, 1] 44 rigid atoms, others: [32, 33, 34, 35, 36, 17, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 127 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074836 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074836 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074836/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074836 Building REAL250005074837 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074837' /scratch/stefan/7916156/working/building/REAL250005074837 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074837 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074837/0 /scratch/stefan/7916156/working/building/REAL250005074837 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 959) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/959 `/scratch/stefan/7916156/working/3D/959' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C(C)(C)O) `REAL250005074837.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074837/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074837 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C(C)(C)O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 20, 9, 1, 9, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 41, 41, 41, 67, 67, 67, 21, 21, 21, 20, 20, 1, 21, 21, 41, 67, 67, 67, 67, 67, 67, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 441 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074837 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C(C)(C)O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 20, 20, 20, 20, 20, 1, 1, 1, 1, 5, 5, 5, 24, 24, 24, 2, 2, 2, 1, 1, 21, 1, 1, 5, 24, 24, 24, 24, 24, 24, 72] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 26, 27, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 190 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074837 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074837 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074837/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074837 Building REAL250005074838 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074838' /scratch/stefan/7916156/working/building/REAL250005074838 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074838 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074838/0 /scratch/stefan/7916156/working/building/REAL250005074838 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 960) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/960 `/scratch/stefan/7916156/working/3D/960' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC1C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005074838.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074838/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074838 none CC1=CC1C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 104 conformations in input total number of sets (complete confs): 104 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 39, 5, 5, 5, 1, 1, 1, 1, 1, 1, 6, 6, 25, 26, 26, 25, 25, 1, 1, 1, 1, 39, 39, 39, 39, 39, 5, 1, 1, 26, 1, 1, 2, 2, 2] 104 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 31, 34, 35, 36]) total number of confs: 135 number of broken/clashed sets: 11 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074838 none CC1=CC1C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 13, 13, 13, 39, 39, 39, 39, 80, 80, 104, 104, 104, 104, 104, 39, 39, 39, 39, 2, 2, 2, 1, 1, 13, 39, 39, 104, 39, 39, 39, 39, 39] 104 rigid atoms, others: [0, 1, 2, 3, 4, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 272 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.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: REAL250005074838 none CC1=CC1C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 48, 48, 48, 26, 26, 26, 25, 9, 1, 9, 1, 1, 1, 1, 1, 1, 25, 26, 26, 26, 104, 104, 104, 104, 104, 48, 25, 25, 1, 26, 26, 26, 26, 26] 104 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36]) total number of confs: 286 number of broken/clashed sets: 11 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074838 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074838 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074838/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074838 Building REAL250005074839 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074839' /scratch/stefan/7916156/working/building/REAL250005074839 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074839 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074839/0 /scratch/stefan/7916156/working/building/REAL250005074839 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 961) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/961 `/scratch/stefan/7916156/working/3D/961' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005074839.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074839/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074839 none C[C@@H](O)C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 159 conformations in input total number of sets (complete confs): 159 using faster count positions algorithm for large data unique positions, atoms: [53, 45, 53, 53, 45, 45, 30, 30, 30, 30, 10, 1, 10, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 53, 53, 53, 159, 45, 30, 30, 1, 30, 30, 30, 30, 30] 159 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 306 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074839 none C[C@@H](O)C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 159 conformations in input total number of sets (complete confs): 159 using faster count positions algorithm for large data unique positions, atoms: [26, 5, 26, 26, 5, 5, 1, 1, 1, 1, 1, 1, 6, 6, 30, 30, 30, 30, 30, 1, 1, 1, 1, 26, 26, 26, 78, 5, 1, 1, 30, 1, 1, 2, 2, 2] 159 rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 28, 29, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 30, 33, 34, 35]) total number of confs: 212 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074839 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074839 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074839/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074839 Building REAL250005074840 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074840' /scratch/stefan/7916156/working/building/REAL250005074840 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074840 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074840/0 /scratch/stefan/7916156/working/building/REAL250005074840 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 962) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/962 `/scratch/stefan/7916156/working/3D/962' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C=CCO) `REAL250005074840.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074840/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074840 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C=CCO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 1, 1, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 297 conformations in input total number of sets (complete confs): 297 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 27, 8, 1, 8, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 58, 58, 58, 96, 96, 99, 28, 28, 28, 27, 27, 1, 28, 28, 58, 96, 96, 99, 99, 297] 297 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 581 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074840 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C=CCO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 1, 1, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 297 conformations in input total number of sets (complete confs): 297 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 27, 27, 27, 27, 27, 1, 1, 1, 1, 5, 5, 5, 24, 24, 63, 2, 2, 2, 1, 1, 28, 1, 1, 5, 24, 24, 63, 63, 189] 297 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 26, 27, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 31, 32, 33, 34, 35, 36]) total number of confs: 455 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074840 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074840 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074840/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074840 Building REAL250005074841 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074841' /scratch/stefan/7916156/working/building/REAL250005074841 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074841 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074841/0 /scratch/stefan/7916156/working/building/REAL250005074841 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 963) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/963 `/scratch/stefan/7916156/working/3D/963' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C1=CCC1) `REAL250005074841.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074841/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074841 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C1=CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 9, 1, 9, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 29, 29, 29, 29, 29, 29, 20, 20, 20, 20, 20, 1, 20, 20, 29, 29, 29, 29, 29, 29] 29 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 70 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074841 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C1=CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 20, 20, 20, 20, 20, 1, 1, 1, 1, 5, 5, 5, 12, 12, 12, 2, 2, 2, 1, 1, 20, 1, 1, 5, 12, 12, 12, 12, 12] 29 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 26, 27, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 31, 32, 33, 34, 35, 36]) total number of confs: 60 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.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: REAL250005074841 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C1=CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 12, 12, 22, 22, 29, 29, 29, 29, 29, 12, 7, 12, 7, 1, 7, 1, 1, 1, 1, 12, 12, 12, 12, 12, 29, 12, 12, 7, 1, 1, 1, 1, 1] 29 rigid atoms, others: [32, 33, 34, 35, 36, 17, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 74 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074841 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074841 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074841/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074841 Building REAL250005074842 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074842' /scratch/stefan/7916156/working/building/REAL250005074842 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074842 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074842/0 /scratch/stefan/7916156/working/building/REAL250005074842 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 964) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/964 `/scratch/stefan/7916156/working/3D/964' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CON=CC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005074842.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074842/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074842 none CON=CC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 8, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 31, 31, 31, 20, 20, 20, 20, 8, 1, 8, 1, 1, 1, 1, 1, 1, 19, 19, 20, 20, 39, 39, 39, 39, 31, 20, 20, 1, 20, 20, 20, 20, 20] 39 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 112 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074842 none CON=CC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 8, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [24, 17, 17, 5, 5, 5, 1, 1, 1, 1, 1, 1, 6, 7, 19, 20, 20, 20, 20, 1, 1, 1, 1, 24, 24, 24, 17, 5, 1, 1, 19, 1, 1, 2, 2, 2] 39 rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 28, 29, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 30, 33, 34, 35]) total number of confs: 92 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074842 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074842 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074842/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074842 Building REAL250005074843 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074843' /scratch/stefan/7916156/working/building/REAL250005074843 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074843 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074843/0 /scratch/stefan/7916156/working/building/REAL250005074843 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 965) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/965 `/scratch/stefan/7916156/working/3D/965' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C1(F)CC1) `REAL250005074843.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074843/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074843 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C1(F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 30, 30, 10, 1, 10, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 61, 61, 61, 82, 82, 82, 30, 30, 30, 30, 30, 1, 30, 30, 61, 82, 82, 82, 82] 82 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 226 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074843 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C1(F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 30, 30, 30, 30, 30, 1, 1, 1, 1, 5, 5, 5, 31, 31, 31, 2, 2, 2, 1, 1, 30, 1, 1, 5, 31, 31, 31, 31] 82 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 26, 27, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 31, 32, 33, 34, 35]) total number of confs: 119 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.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: REAL250005074843 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C1(F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 31, 31, 31, 31, 68, 68, 82, 82, 82, 82, 82, 31, 13, 31, 13, 1, 13, 1, 1, 1, 1, 31, 31, 31, 31, 31, 82, 31, 31, 13, 1, 1, 1, 1] 82 rigid atoms, others: [32, 33, 34, 35, 17, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 222 number of broken/clashed sets: 5 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074843 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074843 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074843/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074843 Building REAL250005074844 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074844' /scratch/stefan/7916156/working/building/REAL250005074844 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074844 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074844/0 /scratch/stefan/7916156/working/building/REAL250005074844 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 966) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/966 `/scratch/stefan/7916156/working/3D/966' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=C(F)C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005074844.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074844/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074844 none CC=C(F)C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 36, 46, 36, 36, 23, 23, 23, 23, 9, 1, 9, 1, 1, 1, 1, 1, 1, 22, 22, 23, 23, 46, 46, 46, 46, 36, 23, 23, 1, 23, 23, 23, 23, 23] 46 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 130 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074844 none CC=C(F)C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 5, 20, 5, 5, 1, 1, 1, 1, 1, 1, 6, 7, 22, 23, 23, 23, 23, 1, 1, 1, 1, 21, 21, 21, 21, 5, 1, 1, 22, 1, 1, 2, 2, 2] 46 rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 28, 29, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 30, 33, 34, 35]) total number of confs: 92 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074844 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074844 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074844/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074844 Building REAL250005074845 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074845' /scratch/stefan/7916156/working/building/REAL250005074845 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074845 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074845/0 /scratch/stefan/7916156/working/building/REAL250005074845 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 967) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/967 `/scratch/stefan/7916156/working/3D/967' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CO)C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005074845.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074845/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074845 none CC(CO)C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 369 conformations in input total number of sets (complete confs): 369 using faster count positions algorithm for large data unique positions, atoms: [119, 56, 119, 123, 56, 56, 27, 27, 27, 27, 10, 1, 10, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 119, 119, 119, 119, 123, 123, 369, 56, 27, 27, 1, 27, 27, 27, 27, 27] 369 rigid atoms, others: [33, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38]) total number of confs: 833 number of broken/clashed sets: 48 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074845 none CC(CO)C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 369 conformations in input total number of sets (complete confs): 369 using faster count positions algorithm for large data unique positions, atoms: [29, 5, 29, 60, 5, 5, 1, 1, 1, 1, 1, 1, 6, 7, 27, 26, 27, 27, 27, 1, 1, 1, 1, 29, 29, 29, 29, 60, 60, 180, 5, 1, 1, 27, 1, 1, 2, 2, 2] 369 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 33, 36, 37, 38]) total number of confs: 458 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074845 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074845 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074845/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074845 Building REAL250005074846 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074846' /scratch/stefan/7916156/working/building/REAL250005074846 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074846 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074846/0 /scratch/stefan/7916156/working/building/REAL250005074846 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 968) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/968 `/scratch/stefan/7916156/working/3D/968' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005074846.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074846/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074846 none C[C@H](O)C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 40, 50, 50, 40, 40, 25, 25, 25, 25, 9, 1, 9, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 50, 50, 50, 150, 40, 25, 25, 1, 25, 25, 25, 25, 25] 150 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 301 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074846 none C[C@H](O)C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [24, 5, 24, 24, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 25, 25, 25, 25, 25, 1, 1, 1, 1, 24, 24, 24, 72, 5, 1, 1, 25, 1, 1, 2, 2, 2] 150 rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 28, 29, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 30, 33, 34, 35]) total number of confs: 196 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074846 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074846 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074846/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074846 Building REAL250005074847 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074847' /scratch/stefan/7916156/working/building/REAL250005074847 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074847 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074847/0 /scratch/stefan/7916156/working/building/REAL250005074847 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 969) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/969 `/scratch/stefan/7916156/working/3D/969' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C1CC1C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005074847.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074847/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074847 none C=C1CC1C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 38, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 30, 30, 30, 30, 30, 1, 1, 1, 1, 38, 38, 38, 38, 38, 5, 1, 1, 30, 1, 1, 2, 2, 2] 94 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 31, 34, 35, 36]) total number of confs: 134 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074847 none C=C1CC1C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 13, 13, 13, 38, 38, 38, 38, 78, 78, 94, 94, 94, 94, 94, 38, 38, 38, 38, 1, 1, 1, 1, 1, 13, 38, 38, 94, 38, 38, 38, 38, 38] 94 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 25, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 251 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.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: REAL250005074847 none C=C1CC1C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [94, 94, 94, 47, 47, 47, 30, 30, 30, 30, 10, 1, 10, 1, 1, 1, 1, 1, 1, 29, 30, 30, 30, 94, 94, 94, 94, 94, 47, 30, 30, 1, 30, 30, 30, 30, 30] 94 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36]) total number of confs: 260 number of broken/clashed sets: 10 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074847 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074847 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074847/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074847 Building REAL250005074848 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074848' /scratch/stefan/7916156/working/building/REAL250005074848 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074848 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074848/0 /scratch/stefan/7916156/working/building/REAL250005074848 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 970) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/970 `/scratch/stefan/7916156/working/3D/970' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CF)C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005074848.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074848/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074848 none CC(CF)C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [122, 58, 122, 125, 58, 58, 24, 24, 24, 24, 10, 1, 10, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 122, 122, 122, 122, 125, 125, 58, 24, 24, 1, 24, 24, 24, 24, 24] 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, 33, 34, 35, 36, 37]) total number of confs: 445 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074848 none CC(CF)C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [35, 5, 35, 67, 5, 5, 1, 1, 1, 1, 1, 1, 6, 6, 24, 24, 24, 24, 24, 1, 1, 1, 1, 35, 35, 35, 35, 67, 67, 5, 1, 1, 24, 1, 1, 2, 2, 2] 125 rigid atoms, others: [33, 34, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 32, 35, 36, 37]) total number of confs: 307 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074848 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074848 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074848/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074848 Building REAL250005074849 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074849' /scratch/stefan/7916156/working/building/REAL250005074849 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074849 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074849/0 /scratch/stefan/7916156/working/building/REAL250005074849 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 971) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/971 `/scratch/stefan/7916156/working/3D/971' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)CC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005074849.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074849.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074849/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074849 none C=C(C)CC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [108, 108, 108, 56, 56, 56, 29, 29, 29, 29, 10, 1, 10, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 108, 108, 108, 108, 108, 108, 108, 56, 29, 29, 1, 29, 29, 29, 29, 29] 108 rigid atoms, others: [33, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38]) total number of confs: 383 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074849 none C=C(C)CC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [55, 38, 55, 5, 5, 5, 1, 1, 1, 1, 1, 1, 6, 6, 29, 29, 29, 29, 29, 1, 1, 1, 1, 55, 55, 55, 55, 55, 38, 38, 5, 1, 1, 29, 1, 1, 2, 2, 2] 108 rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 33, 36, 37, 38]) total number of confs: 231 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074849 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074849 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074849/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074849 Building REAL250005074850 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074850' /scratch/stefan/7916156/working/building/REAL250005074850 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074850 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074850/0 /scratch/stefan/7916156/working/building/REAL250005074850 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 972) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/972 `/scratch/stefan/7916156/working/3D/972' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005074850.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074850/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074850 none CC=CC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 32, 32, 32, 22, 22, 22, 22, 8, 1, 8, 1, 1, 1, 1, 1, 1, 21, 21, 22, 22, 42, 42, 42, 42, 42, 32, 22, 22, 1, 22, 22, 22, 22, 22] 42 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 126 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074850 none CC=CC(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 5, 5, 5, 1, 1, 1, 1, 1, 1, 6, 7, 21, 22, 22, 22, 22, 1, 1, 1, 1, 20, 20, 20, 20, 20, 5, 1, 1, 21, 1, 1, 2, 2, 2] 42 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 28, 29, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 30, 33, 34, 35]) total number of confs: 88 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074850 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074850 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074850/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074850 Building REAL250005074851 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074851' /scratch/stefan/7916156/working/building/REAL250005074851 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074851 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074851/0 /scratch/stefan/7916156/working/building/REAL250005074851 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 973) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/973 `/scratch/stefan/7916156/working/3D/973' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H]1C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C) `REAL250005074851.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074851/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074851 none C[C@@H]1C[C@H]1C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 32, 32, 5, 32, 5, 5, 1, 1, 1, 1, 1, 1, 6, 6, 27, 28, 28, 28, 28, 1, 1, 1, 1, 32, 32, 32, 32, 32, 5, 1, 1, 27, 1, 1, 2, 2, 2] 78 rigid atoms, others: [32, 34, 35, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 33, 36, 37, 38]) total number of confs: 120 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074851 none C[C@@H]1C[C@H]1C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 13, 13, 13, 32, 32, 32, 32, 67, 67, 78, 78, 78, 78, 78, 32, 32, 32, 32, 2, 2, 2, 1, 1, 13, 32, 32, 78, 32, 32, 32, 32, 32] 78 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 218 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.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: REAL250005074851 none C[C@@H]1C[C@H]1C(=O)N[C@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 46, 78, 46, 46, 27, 27, 27, 27, 9, 1, 9, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 78, 78, 78, 78, 78, 46, 27, 27, 1, 27, 27, 28, 28, 28] 78 rigid atoms, others: [33, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38]) total number of confs: 223 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074851 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074851 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074851/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074851 Building REAL250005074852 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074852' /scratch/stefan/7916156/working/building/REAL250005074852 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074852 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074852/0 /scratch/stefan/7916156/working/building/REAL250005074852 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 974) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/974 `/scratch/stefan/7916156/working/3D/974' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C1(O)CC1) `REAL250005074852.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074852/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074852 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C1(O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 219 conformations in input total number of sets (complete confs): 219 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 30, 30, 10, 1, 10, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 61, 61, 61, 73, 73, 73, 30, 30, 30, 30, 30, 1, 30, 30, 61, 219, 73, 73, 73, 73] 219 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 419 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074852 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C1(O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 219 conformations in input total number of sets (complete confs): 219 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 30, 30, 30, 30, 30, 1, 1, 1, 1, 5, 5, 5, 30, 30, 30, 2, 2, 2, 1, 1, 30, 1, 1, 5, 90, 30, 30, 30, 30] 219 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 26, 27, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 31, 32, 33, 34, 35, 36]) total number of confs: 207 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.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: REAL250005074852 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@@H]1NC(=O)C1(O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 219 conformations in input total number of sets (complete confs): 219 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 30, 30, 30, 30, 61, 61, 73, 73, 73, 73, 73, 30, 11, 30, 11, 1, 11, 1, 1, 1, 1, 30, 30, 30, 30, 30, 73, 30, 30, 11, 6, 1, 1, 1, 1] 219 rigid atoms, others: [33, 34, 35, 36, 17, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 210 number of broken/clashed sets: 9 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074852 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074852 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074852/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074852 Building REAL250005074853 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074853' /scratch/stefan/7916156/working/building/REAL250005074853 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074853 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074853/0 /scratch/stefan/7916156/working/building/REAL250005074853 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 975) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/975 `/scratch/stefan/7916156/working/3D/975' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)CC2CC2)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005074853.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074853/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074853 none C[C@@H]1CN(C(=O)CC2CC2)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [42, 42, 42, 42, 17, 3, 17, 1, 1, 1, 1, 42, 42, 42, 42, 65, 65, 65, 76, 76, 76, 76, 76, 42, 42, 42, 42, 42, 3, 3, 1, 1, 1, 1, 1, 42, 42, 65, 76] 76 rigid atoms, others: [32, 33, 34, 7, 8, 9, 10, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38]) total number of confs: 192 number of broken/clashed sets: 14 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074853 none C[C@@H]1CN(C(=O)CC2CC2)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 30, 42, 42, 1, 1, 1, 1, 5, 5, 5, 14, 14, 14, 14, 14, 2, 2, 2, 1, 1, 30, 30, 42, 42, 42, 42, 42, 1, 1, 5, 14] 76 rigid atoms, others: [0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 35, 36, 26, 27] set([6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 37, 38]) total number of confs: 178 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.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: REAL250005074853 none C[C@@H]1CN(C(=O)CC2CC2)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [14, 14, 14, 14, 14, 14, 35, 35, 70, 76, 76, 14, 7, 14, 7, 1, 7, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 70, 70, 76, 76, 76, 76, 76, 14, 14, 7, 1] 76 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: 294 number of broken/clashed sets: 14 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074853 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074853 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074853/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074853 Building REAL250005074854 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074854' /scratch/stefan/7916156/working/building/REAL250005074854 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074854 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074854/0 /scratch/stefan/7916156/working/building/REAL250005074854 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 976) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/976 `/scratch/stefan/7916156/working/3D/976' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C(C)(C)F)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005074854.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074854/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074854 none C[C@@H]1CN(C(=O)C(C)(C)F)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 15, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 9, 9, 16, 16, 23, 23, 23, 9, 6, 9, 6, 1, 6, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 23, 23, 23, 23, 23, 23, 9, 9, 6, 1] 23 rigid atoms, others: [37, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 89 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074854 none C[C@@H]1CN(C(=O)C(C)(C)F)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 15, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 17, 17, 17, 1, 1, 1, 1, 5, 5, 5, 9, 9, 9, 9, 9, 2, 2, 2, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1, 5, 9] 23 rigid atoms, others: [0, 1, 2, 3, 4, 5, 11, 12, 34, 14, 13, 35, 26, 27] set([6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 36, 37]) total number of confs: 86 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074854 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074854 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074854/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074854 Building REAL250005074855 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074855' /scratch/stefan/7916156/working/building/REAL250005074855 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074855 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074855/0 /scratch/stefan/7916156/working/building/REAL250005074855 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 977) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/977 `/scratch/stefan/7916156/working/3D/977' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074855.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074855.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074855/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074855 none COCC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [39, 38, 21, 9, 21, 9, 9, 9, 9, 9, 4, 9, 4, 1, 4, 1, 1, 1, 1, 1, 1, 9, 39, 39, 39, 38, 38, 9, 9, 9, 9, 9, 4, 1, 9, 9] 39 rigid atoms, others: [33, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35]) total number of confs: 145 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074855 none COCC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [28, 14, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 9, 9, 9, 9, 1, 29, 29, 29, 14, 14, 1, 1, 2, 2, 2, 5, 9, 1, 1] 39 rigid atoms, others: [34, 3, 5, 6, 7, 8, 9, 10, 11, 12, 35, 21, 27, 28] set([0, 1, 2, 4, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 100 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074855 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074855 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074855/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074855 Building REAL250005074856 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074856' /scratch/stefan/7916156/working/building/REAL250005074856 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074856 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074856/0 /scratch/stefan/7916156/working/building/REAL250005074856 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 978) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/978 `/scratch/stefan/7916156/working/3D/978' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074856.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074856/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074856 none CCCC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [53, 52, 31, 15, 31, 15, 15, 15, 15, 15, 7, 15, 7, 1, 7, 1, 1, 1, 1, 1, 1, 15, 53, 53, 53, 53, 53, 52, 52, 15, 15, 15, 15, 15, 7, 1, 15, 15] 53 rigid atoms, others: [35, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37]) total number of confs: 200 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074856 none CCCC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [31, 24, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 15, 15, 15, 1, 32, 32, 32, 31, 31, 24, 24, 1, 1, 2, 2, 2, 5, 15, 1, 1] 53 rigid atoms, others: [3, 36, 5, 6, 7, 8, 9, 10, 11, 12, 21, 29, 30, 37] set([0, 1, 2, 4, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35]) total number of confs: 163 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074856 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074856 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074856/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074856 Building REAL250005074857 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074857' /scratch/stefan/7916156/working/building/REAL250005074857 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074857 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074857/0 /scratch/stefan/7916156/working/building/REAL250005074857 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 979) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/979 `/scratch/stefan/7916156/working/3D/979' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074857.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074857/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074857 none CC(C)CC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [45, 46, 46, 28, 13, 28, 13, 13, 13, 13, 13, 7, 13, 7, 1, 7, 1, 1, 1, 1, 1, 1, 13, 46, 46, 46, 46, 46, 46, 46, 46, 46, 13, 13, 13, 13, 13, 8, 1, 13, 13] 46 rigid atoms, others: [38, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40]) total number of confs: 171 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074857 none CC(C)CC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [23, 22, 27, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 13, 13, 13, 13, 1, 27, 27, 27, 27, 27, 27, 27, 22, 22, 1, 1, 2, 2, 2, 5, 13, 1, 1] 46 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 11, 12, 13, 40, 22, 39] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38]) total number of confs: 157 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074857 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074857 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074857/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074857 Building REAL250005074858 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074858' /scratch/stefan/7916156/working/building/REAL250005074858 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074858 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074858/0 /scratch/stefan/7916156/working/building/REAL250005074858 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 980) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/980 `/scratch/stefan/7916156/working/3D/980' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC1C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074858.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074858/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074858 none CC1CC1C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 12, 12, 12, 12, 1, 15, 15, 15, 15, 15, 15, 15, 1, 1, 2, 2, 2, 5, 12, 1, 1] 23 rigid atoms, others: [4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 22, 38, 30, 31] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 66 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074858 none CC1CC1C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 6, 6, 15, 15, 15, 15, 15, 15, 15, 21, 21, 21, 23, 23, 23, 23, 23, 15, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 21, 23, 15, 15] 23 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 25, 26, 27, 28, 29] set([5, 6, 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: 51 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.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: REAL250005074858 none CC1CC1C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 18, 12, 18, 12, 12, 12, 12, 12, 7, 12, 7, 1, 7, 1, 1, 1, 1, 1, 1, 12, 23, 23, 23, 23, 23, 23, 23, 12, 12, 12, 12, 12, 7, 1, 12, 12] 23 rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 65 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074858 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074858 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074858/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074858 Building REAL250005074859 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074859' /scratch/stefan/7916156/working/building/REAL250005074859 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074859 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074859/0 /scratch/stefan/7916156/working/building/REAL250005074859 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 981) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/981 `/scratch/stefan/7916156/working/3D/981' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074859.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074859/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074859 none CCOCC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [102, 100, 87, 39, 16, 39, 16, 16, 16, 16, 16, 7, 16, 7, 1, 7, 1, 1, 1, 1, 1, 1, 16, 102, 102, 102, 102, 102, 87, 87, 16, 16, 16, 16, 16, 7, 1, 16, 16] 102 rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 347 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074859 none CCOCC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [86, 75, 35, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 16, 16, 16, 16, 16, 1, 86, 86, 86, 86, 86, 35, 35, 1, 1, 2, 2, 2, 5, 16, 1, 1] 102 rigid atoms, others: [4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 22, 38, 30, 31] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 272 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074859 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074859 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074859/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074859 Building REAL250005074860 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074860' /scratch/stefan/7916156/working/building/REAL250005074860 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074860 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074860/0 /scratch/stefan/7916156/working/building/REAL250005074860 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 982) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/982 `/scratch/stefan/7916156/working/3D/982' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)=CC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074860.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074860/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074860 none CC(C)=CC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 21, 11, 21, 11, 11, 11, 11, 11, 6, 11, 6, 1, 6, 1, 1, 1, 1, 1, 1, 11, 33, 33, 33, 33, 33, 33, 33, 11, 11, 11, 11, 11, 6, 1, 11, 11] 33 rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 109 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074860 none CC(C)=CC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 11, 11, 11, 11, 11, 1, 20, 20, 20, 20, 20, 20, 20, 1, 1, 2, 2, 2, 5, 11, 1, 1] 33 rigid atoms, others: [4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 22, 38, 30, 31] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 78 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074860 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074860 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074860/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074860 Building REAL250005074861 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074861' /scratch/stefan/7916156/working/building/REAL250005074861 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074861 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074861/0 /scratch/stefan/7916156/working/building/REAL250005074861 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 983) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/983 `/scratch/stefan/7916156/working/3D/983' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSCC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074861.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074861/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074861 none CSCC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [60, 47, 25, 11, 25, 11, 11, 11, 11, 11, 4, 11, 4, 1, 4, 1, 1, 1, 1, 1, 1, 11, 60, 60, 60, 47, 47, 11, 11, 11, 11, 11, 4, 1, 11, 11] 60 rigid atoms, others: [33, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35]) total number of confs: 203 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074861 none CSCC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [53, 26, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 11, 11, 11, 11, 11, 1, 53, 53, 53, 26, 26, 1, 1, 2, 2, 2, 5, 11, 1, 1] 60 rigid atoms, others: [34, 3, 5, 6, 7, 8, 9, 10, 11, 12, 35, 21, 27, 28] set([0, 1, 2, 4, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 153 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074861 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074861 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074861/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074861 Building REAL250005074862 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074862' /scratch/stefan/7916156/working/building/REAL250005074862 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074862 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074862/0 /scratch/stefan/7916156/working/building/REAL250005074862 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 984) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/984 `/scratch/stefan/7916156/working/3D/984' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074862.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074862/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074862 none CCCCC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [118, 113, 99, 44, 16, 44, 16, 16, 16, 16, 16, 7, 16, 7, 1, 7, 1, 1, 1, 1, 1, 1, 16, 118, 118, 118, 118, 118, 113, 113, 99, 99, 16, 16, 16, 16, 16, 7, 1, 16, 16] 118 rigid atoms, others: [38, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40]) total number of confs: 484 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074862 none CCCCC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [71, 49, 34, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 16, 16, 16, 16, 16, 1, 71, 72, 72, 70, 69, 53, 53, 35, 35, 1, 1, 2, 2, 2, 5, 16, 1, 1] 118 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 11, 12, 13, 40, 22, 39] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38]) total number of confs: 370 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074862 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074862 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074862/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074862 Building REAL250005074863 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074863' /scratch/stefan/7916156/working/building/REAL250005074863 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074863 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074863/0 /scratch/stefan/7916156/working/building/REAL250005074863 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 985) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/985 `/scratch/stefan/7916156/working/3D/985' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074863.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074863.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074863/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074863 none CC(C)C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 13, 23, 13, 13, 13, 13, 13, 6, 13, 6, 1, 6, 1, 1, 1, 1, 1, 1, 13, 23, 23, 23, 23, 23, 23, 23, 13, 13, 13, 13, 13, 6, 1, 13, 13] 23 rigid atoms, others: [35, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37]) total number of confs: 71 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074863 none CC(C)C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 12, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 13, 13, 13, 13, 1, 12, 12, 12, 12, 12, 12, 12, 1, 1, 2, 2, 2, 5, 13, 1, 1] 23 rigid atoms, others: [3, 36, 5, 6, 7, 8, 9, 10, 11, 12, 21, 29, 30, 37] set([0, 1, 2, 4, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35]) total number of confs: 71 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074863 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074863 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074863/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074863 Building REAL250005074864 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074864' /scratch/stefan/7916156/working/building/REAL250005074864 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074864 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074864/0 /scratch/stefan/7916156/working/building/REAL250005074864 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 986) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/986 `/scratch/stefan/7916156/working/3D/986' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074864.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074864/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074864 none CCC(C)C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [45, 44, 33, 44, 15, 33, 15, 15, 15, 15, 15, 6, 15, 6, 1, 6, 1, 1, 1, 1, 1, 1, 15, 45, 45, 45, 45, 45, 44, 44, 44, 44, 15, 15, 15, 15, 15, 7, 1, 15, 15] 45 rigid atoms, others: [38, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40]) total number of confs: 158 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074864 none CCC(C)C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [28, 20, 7, 20, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 15, 15, 14, 1, 29, 29, 29, 29, 29, 20, 20, 20, 20, 1, 1, 2, 2, 2, 5, 15, 1, 1] 45 rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 11, 12, 13, 40, 22, 39] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38]) total number of confs: 159 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074864 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074864 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074864/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074864 Building REAL250005074865 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074865' /scratch/stefan/7916156/working/building/REAL250005074865 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074865 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074865/0 /scratch/stefan/7916156/working/building/REAL250005074865 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 987) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/987 `/scratch/stefan/7916156/working/3D/987' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074865.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074865/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074865 none COC(C)C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 24, 35, 8, 24, 8, 8, 8, 8, 8, 4, 8, 4, 1, 4, 1, 1, 1, 1, 1, 1, 8, 35, 35, 35, 35, 35, 35, 35, 8, 8, 8, 8, 8, 4, 1, 8, 8] 35 rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 121 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074865 none COC(C)C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [26, 20, 7, 20, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 8, 8, 8, 1, 26, 26, 26, 20, 20, 20, 20, 1, 1, 2, 2, 2, 5, 8, 1, 1] 35 rigid atoms, others: [4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 22, 38, 30, 31] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 105 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074865 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074865 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074865/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074865 Building REAL250005074866 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074866' /scratch/stefan/7916156/working/building/REAL250005074866 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074866 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074866/0 /scratch/stefan/7916156/working/building/REAL250005074866 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 988) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/988 `/scratch/stefan/7916156/working/3D/988' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074866.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074866.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074866/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074866 none C=CCCC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [118, 118, 95, 44, 19, 44, 19, 19, 19, 19, 19, 8, 19, 8, 1, 8, 1, 1, 1, 1, 1, 1, 19, 118, 118, 118, 118, 118, 95, 95, 19, 19, 19, 19, 19, 8, 1, 19, 19] 118 rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 470 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074866 none C=CCCC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [95, 58, 34, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 19, 19, 19, 19, 19, 1, 95, 95, 95, 58, 58, 34, 34, 1, 1, 2, 2, 2, 5, 19, 1, 1] 118 rigid atoms, others: [4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 22, 38, 30, 31] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 405 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074866 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074866 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074866/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074866 Building REAL250005074867 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074867' /scratch/stefan/7916156/working/building/REAL250005074867 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074867 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074867/0 /scratch/stefan/7916156/working/building/REAL250005074867 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 989) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/989 `/scratch/stefan/7916156/working/3D/989' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C#N)C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074867.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074867.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074867/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074867 none CC(C#N)C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.1', 'N.1', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 16, 23, 23, 12, 16, 12, 12, 12, 12, 12, 5, 12, 5, 1, 5, 1, 1, 1, 1, 1, 1, 12, 23, 23, 23, 23, 12, 12, 12, 12, 12, 6, 1, 12, 12] 23 rigid atoms, others: [33, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35]) total number of confs: 89 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074867 none CC(C#N)C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.1', 'N.1', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [15, 7, 15, 15, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 12, 12, 12, 12, 1, 15, 15, 15, 15, 1, 1, 2, 2, 2, 5, 12, 1, 1] 23 rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 22, 27, 28] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 78 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074867 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074867 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074867/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074867 Building REAL250005074868 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074868' /scratch/stefan/7916156/working/building/REAL250005074868 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074868 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074868/0 /scratch/stefan/7916156/working/building/REAL250005074868 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 990) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/990 `/scratch/stefan/7916156/working/3D/990' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=C(C)C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074868.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074868.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074868/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074868 none CC=C(C)C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 32, 45, 13, 32, 13, 13, 13, 13, 13, 6, 13, 6, 1, 6, 1, 1, 1, 1, 1, 1, 13, 45, 45, 45, 45, 45, 45, 45, 13, 13, 13, 13, 13, 7, 1, 13, 13] 45 rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 143 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074868 none CC=C(C)C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 7, 29, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 13, 13, 13, 13, 1, 29, 29, 29, 29, 29, 29, 29, 1, 1, 2, 2, 2, 5, 13, 1, 1] 45 rigid atoms, others: [4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 22, 38, 30, 31] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 99 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074868 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074868 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074868/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074868 Building REAL250005074869 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074869' /scratch/stefan/7916156/working/building/REAL250005074869 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074869 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074869/0 /scratch/stefan/7916156/working/building/REAL250005074869 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 991) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/991 `/scratch/stefan/7916156/working/3D/991' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074869.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074869/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074869 none CCC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [25, 22, 16, 22, 16, 16, 16, 16, 16, 8, 16, 8, 1, 8, 1, 1, 1, 1, 1, 1, 16, 25, 25, 25, 25, 25, 16, 16, 16, 16, 16, 8, 1, 16, 16] 25 rigid atoms, others: [32, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34]) total number of confs: 83 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074869 none CCC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 16, 16, 16, 16, 16, 1, 12, 12, 12, 12, 12, 1, 1, 2, 2, 2, 5, 16, 1, 1] 25 rigid atoms, others: [33, 2, 4, 5, 6, 7, 8, 9, 10, 11, 34, 20, 26, 27] set([0, 1, 3, 32, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30, 31]) total number of confs: 74 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074869 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074869 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074869/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074869 Building REAL250005074870 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074870' /scratch/stefan/7916156/working/building/REAL250005074870 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074870 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074870/0 /scratch/stefan/7916156/working/building/REAL250005074870 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 992) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/992 `/scratch/stefan/7916156/working/3D/992' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074870.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074870/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074870 none COCCC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [93, 93, 80, 40, 18, 40, 18, 18, 18, 18, 18, 8, 18, 8, 1, 8, 1, 1, 1, 1, 1, 1, 18, 93, 93, 93, 93, 93, 80, 80, 18, 18, 18, 18, 18, 8, 1, 18, 18] 93 rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 363 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074870 none COCCC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [73, 51, 30, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 18, 18, 18, 18, 18, 1, 74, 73, 73, 51, 51, 30, 30, 1, 1, 2, 2, 2, 5, 18, 1, 1] 93 rigid atoms, others: [4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 22, 38, 30, 31] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 289 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074870 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074870 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074870/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074870 Building REAL250005074871 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074871' /scratch/stefan/7916156/working/building/REAL250005074871 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074871 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074871/0 /scratch/stefan/7916156/working/building/REAL250005074871 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 993) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/993 `/scratch/stefan/7916156/working/3D/993' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074871.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074871/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074871 none CC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 9, 6, 6, 6, 6, 6, 5, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 9, 9, 9, 6, 6, 6, 6, 6, 5, 1, 6, 6] 9 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: 27 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074871 none CC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 6, 6, 6, 6, 6, 1, 3, 3, 3, 1, 1, 2, 2, 2, 4, 6, 1, 1] 9 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 19, 23, 24, 30, 31] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 25, 26, 27, 28, 29]) total number of confs: 29 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074871 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074871 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074871/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074871 Building REAL250005074872 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074872' /scratch/stefan/7916156/working/building/REAL250005074872 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074872 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074872/0 /scratch/stefan/7916156/working/building/REAL250005074872 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 994) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/994 `/scratch/stefan/7916156/working/3D/994' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2CC2)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005074872.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074872/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074872 none C[C@@H]1CN(C(=O)C2CC2)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 8, 1, 8, 1, 1, 1, 13, 13, 13, 13, 18, 18, 18, 24, 24, 24, 24, 24, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 13, 13, 18, 24] 24 rigid atoms, others: [5, 7, 8, 9, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 32, 33, 34, 35]) total number of confs: 58 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074872 none C[C@@H]1CN(C(=O)C2CC2)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 4, 13, 13, 1, 1, 1, 1, 5, 5, 5, 10, 10, 10, 10, 10, 2, 2, 2, 1, 1, 13, 13, 13, 13, 13, 1, 1, 5, 10] 24 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 10, 11, 12, 13, 33, 25, 26] set([6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 34, 35]) total number of confs: 58 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.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: REAL250005074872 none C[C@@H]1CN(C(=O)C2CC2)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 15, 15, 24, 24, 10, 6, 10, 6, 1, 6, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 24, 24, 24, 24, 24, 10, 10, 7, 1] 24 rigid atoms, others: [35, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 83 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074872 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074872 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074872/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074872 Building REAL250005074873 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074873' /scratch/stefan/7916156/working/building/REAL250005074873 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074873 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074873/0 /scratch/stefan/7916156/working/building/REAL250005074873 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 995) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/995 `/scratch/stefan/7916156/working/3D/995' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2CCC2)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005074873.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074873.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074873/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074873 none C[C@@H]1CN(C(=O)C2CCC2)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 8, 1, 8, 1, 1, 1, 1, 18, 18, 18, 18, 24, 24, 24, 32, 32, 32, 32, 32, 18, 18, 18, 18, 18, 1, 1, 1, 1, 1, 1, 1, 18, 18, 24, 32] 32 rigid atoms, others: [32, 33, 34, 5, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36, 37, 38]) total number of confs: 73 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074873 none C[C@@H]1CN(C(=O)C2CCC2)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 18, 18, 18, 1, 1, 1, 1, 5, 5, 5, 13, 13, 13, 13, 13, 2, 2, 2, 1, 1, 18, 18, 18, 18, 18, 18, 18, 1, 1, 5, 13] 32 rigid atoms, others: [0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 35, 36, 26, 27] set([6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 37, 38]) total number of confs: 77 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.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: REAL250005074873 none C[C@@H]1CN(C(=O)C2CCC2)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 13, 21, 21, 32, 32, 32, 13, 7, 13, 7, 1, 7, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 32, 32, 32, 32, 32, 32, 32, 13, 13, 7, 1] 32 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: 107 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074873 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074873 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074873/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074873 Building REAL250005074874 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074874' /scratch/stefan/7916156/working/building/REAL250005074874 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074874 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074874/0 /scratch/stefan/7916156/working/building/REAL250005074874 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 996) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/996 `/scratch/stefan/7916156/working/3D/996' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C(N)=O)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005074874.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074874.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074874/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074874 none C[C@@H]1CN(C(=O)C(N)=O)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 8, 11, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 4, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 13, 20, 20, 26, 26, 13, 5, 13, 5, 1, 5, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 26, 26, 13, 13, 5, 1] 26 rigid atoms, others: [32, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 81 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074874 none C[C@@H]1CN(C(=O)C(N)=O)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 8, 11, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 4, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 18, 18, 1, 1, 1, 1, 5, 5, 5, 13, 13, 13, 13, 13, 2, 2, 2, 1, 1, 18, 18, 1, 1, 5, 13] 26 rigid atoms, others: [0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 25, 26, 29, 30] set([32, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 31]) total number of confs: 74 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074874 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074874 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074874/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074874 Building REAL250005074875 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074875' /scratch/stefan/7916156/working/building/REAL250005074875 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074875 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074875/0 /scratch/stefan/7916156/working/building/REAL250005074875 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 997) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/997 `/scratch/stefan/7916156/working/3D/997' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C(C)(C)C)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005074875.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074875.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074875/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074875 none C[C@@H]1CN(C(=O)C(C)(C)C)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 9, 5, 3, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 5, 3, 1] 9 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: 27 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074875 none C[C@@H]1CN(C(=O)C(C)(C)C)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 4, 4, 5, 5, 5, 5, 5, 2, 2, 2, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 4, 5] 9 rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 11, 12, 13, 14, 26, 27, 37] set([6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40]) total number of confs: 25 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074875 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074875 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074875/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074875 Building REAL250005074876 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074876' /scratch/stefan/7916156/working/building/REAL250005074876 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074876 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074876/0 /scratch/stefan/7916156/working/building/REAL250005074876 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 998) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/998 `/scratch/stefan/7916156/working/3D/998' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2(C)CC2)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005074876.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074876/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074876 none C[C@@H]1CN(C(=O)C2(C)CC2)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 3, 1, 3, 1, 1, 1, 1, 10, 10, 10, 10, 20, 20, 20, 23, 23, 23, 23, 23, 10, 10, 10, 10, 10, 2, 2, 2, 1, 1, 1, 1, 10, 10, 20, 23] 23 rigid atoms, others: [32, 33, 34, 5, 7, 8, 9, 10, 31] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38]) total number of confs: 66 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074876 none C[C@@H]1CN(C(=O)C2(C)CC2)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 10, 10, 10, 1, 1, 1, 1, 5, 5, 5, 10, 10, 10, 9, 10, 2, 2, 2, 1, 1, 10, 10, 10, 10, 10, 10, 10, 1, 1, 5, 10] 23 rigid atoms, others: [0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 35, 36, 26, 27] set([6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 37, 38]) total number of confs: 54 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.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: REAL250005074876 none C[C@@H]1CN(C(=O)C2(C)CC2)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 21, 21, 23, 23, 23, 10, 6, 10, 6, 1, 6, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 23, 23, 23, 23, 23, 23, 23, 10, 10, 6, 1] 23 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: 71 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074876 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074876 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074876/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074876 Building REAL250005074877 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074877' /scratch/stefan/7916156/working/building/REAL250005074877 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074877 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074877/0 /scratch/stefan/7916156/working/building/REAL250005074877 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 999) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/999 `/scratch/stefan/7916156/working/3D/999' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H]1C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074877.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074877/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074877 none C[C@@H]1C[C@H]1C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 6, 26, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 15, 15, 15, 1, 26, 26, 26, 26, 26, 1, 1, 2, 2, 2, 5, 15, 1, 1] 40 rigid atoms, others: [37, 6, 8, 9, 10, 11, 12, 13, 14, 15, 24, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 95 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074877 none C[C@@H]1C[C@H]1C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 8, 8, 26, 26, 26, 26, 26, 26, 26, 36, 36, 36, 40, 40, 40, 40, 40, 26, 2, 2, 2, 1, 1, 26, 26, 26, 26, 26, 36, 40, 26, 26] 40 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 96 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.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: REAL250005074877 none C[C@@H]1C[C@H]1C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 32, 40, 15, 32, 15, 15, 15, 15, 15, 6, 15, 6, 1, 6, 1, 1, 1, 1, 1, 1, 15, 40, 40, 40, 40, 40, 15, 15, 15, 15, 15, 6, 1, 15, 15] 40 rigid atoms, others: [36, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 127 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074877 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074877 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074877/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074877 Building REAL250005074878 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074878' /scratch/stefan/7916156/working/building/REAL250005074878 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074878 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074878/0 /scratch/stefan/7916156/working/building/REAL250005074878 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 1000) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/1000 `/scratch/stefan/7916156/working/3D/1000' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(F)C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074878.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074878/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074878 none CCC(F)C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 36, 59, 15, 36, 15, 15, 15, 15, 15, 6, 15, 6, 1, 6, 1, 1, 1, 1, 1, 1, 15, 59, 59, 59, 59, 59, 59, 15, 15, 15, 15, 15, 6, 1, 15, 15] 59 rigid atoms, others: [35, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37]) total number of confs: 207 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074878 none CCC(F)C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [38, 29, 6, 29, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 15, 15, 15, 1, 42, 42, 42, 42, 42, 29, 1, 1, 2, 2, 2, 5, 15, 1, 1] 59 rigid atoms, others: [4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 22, 36, 29, 30] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35]) total number of confs: 230 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074878 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074878 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074878/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074878 Building REAL250005074879 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074879' /scratch/stefan/7916156/working/building/REAL250005074879 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074879 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074879/0 /scratch/stefan/7916156/working/building/REAL250005074879 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 1001) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/1001 `/scratch/stefan/7916156/working/3D/1001' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)CCCF)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005074879.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074879/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074879 none C[C@@H]1CN(C(=O)CCCF)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 15, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 106 conformations in input total number of sets (complete confs): 106 using faster count positions algorithm for large data unique positions, atoms: [14, 14, 14, 14, 14, 14, 35, 35, 89, 103, 106, 14, 7, 14, 7, 1, 7, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 89, 89, 106, 106, 106, 106, 14, 14, 7, 1] 106 rigid atoms, others: [37, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 433 number of broken/clashed sets: 14 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074879 none C[C@@H]1CN(C(=O)CCCF)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 15, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 106 conformations in input total number of sets (complete confs): 106 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 29, 39, 79, 1, 1, 1, 1, 5, 5, 5, 14, 14, 14, 14, 14, 2, 2, 2, 1, 1, 29, 29, 48, 48, 71, 75, 1, 1, 5, 14] 106 rigid atoms, others: [0, 1, 2, 3, 4, 5, 11, 12, 34, 14, 13, 35, 26, 27] set([6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 36, 37]) total number of confs: 406 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074879 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074879 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074879/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074879 Building REAL250005074880 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074880' /scratch/stefan/7916156/working/building/REAL250005074880 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074880 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074880/0 /scratch/stefan/7916156/working/building/REAL250005074880 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 1002) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/1002 `/scratch/stefan/7916156/working/3D/1002' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@@H]1C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074880.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074880/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074880 none C[C@H]1C[C@@H]1C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 7, 20, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 13, 13, 13, 13, 1, 20, 20, 20, 20, 20, 1, 1, 2, 2, 2, 5, 13, 1, 1] 33 rigid atoms, others: [37, 6, 8, 9, 10, 11, 12, 13, 14, 15, 24, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 80 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074880 none C[C@H]1C[C@@H]1C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 7, 20, 20, 20, 20, 20, 20, 20, 30, 30, 30, 33, 33, 33, 33, 33, 20, 2, 2, 2, 1, 1, 20, 20, 20, 20, 20, 30, 33, 20, 20] 33 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 84 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.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: REAL250005074880 none C[C@H]1C[C@@H]1C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 30, 33, 13, 30, 13, 13, 13, 13, 13, 7, 13, 7, 1, 7, 1, 1, 1, 1, 1, 1, 13, 33, 33, 33, 33, 33, 13, 13, 13, 13, 13, 7, 1, 13, 13] 33 rigid atoms, others: [36, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 95 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074880 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074880 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074880/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074880 Building REAL250005074881 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074881' /scratch/stefan/7916156/working/building/REAL250005074881 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074881 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074881/0 /scratch/stefan/7916156/working/building/REAL250005074881 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 1003) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/1003 `/scratch/stefan/7916156/working/3D/1003' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)CO)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005074881.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074881/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074881 none C[C@@H]1CN(C(=O)CO)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 12, 12, 12, 16, 16, 18, 12, 6, 12, 6, 1, 6, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 18, 18, 54, 12, 12, 6, 1] 54 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: 113 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074881 none C[C@@H]1CN(C(=O)CO)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 4, 11, 1, 1, 1, 1, 5, 5, 5, 12, 12, 12, 12, 12, 2, 2, 2, 1, 1, 11, 11, 33, 1, 1, 5, 12] 54 rigid atoms, others: [0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 24, 25, 29, 30] set([32, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 31]) total number of confs: 95 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074881 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074881 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074881/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074881 Building REAL250005074882 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074882' /scratch/stefan/7916156/working/building/REAL250005074882 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074882 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074882/0 /scratch/stefan/7916156/working/building/REAL250005074882 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 1004) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/1004 `/scratch/stefan/7916156/working/3D/1004' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2CCO2)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005074882.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074882/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074882 none C[C@@H]1CN(C(=O)C2CCO2)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 8, 1, 8, 1, 1, 1, 1, 23, 23, 23, 23, 31, 31, 31, 32, 32, 32, 32, 32, 23, 23, 23, 23, 23, 1, 1, 1, 1, 1, 23, 23, 31, 32] 32 rigid atoms, others: [32, 5, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35, 36]) total number of confs: 72 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074882 none C[C@@H]1CN(C(=O)C2CCO2)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 23, 23, 23, 1, 1, 1, 1, 5, 5, 5, 12, 12, 12, 12, 12, 2, 2, 2, 1, 1, 23, 23, 23, 23, 23, 1, 1, 5, 12] 32 rigid atoms, others: [0, 1, 2, 3, 4, 5, 33, 11, 12, 34, 14, 13, 26, 27] set([6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 35, 36]) total number of confs: 84 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.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: REAL250005074882 none C[C@@H]1CN(C(=O)C2CCO2)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 12, 12, 25, 25, 32, 32, 32, 12, 5, 12, 5, 1, 5, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 32, 32, 32, 32, 32, 12, 12, 5, 1] 32 rigid atoms, others: [36, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 97 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074882 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074882 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074882/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074882 Building REAL250005074883 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074883' /scratch/stefan/7916156/working/building/REAL250005074883 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074883 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074883/0 /scratch/stefan/7916156/working/building/REAL250005074883 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 1005) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/1005 `/scratch/stefan/7916156/working/3D/1005' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2COC2)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005074883.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074883.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074883/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074883 none C[C@@H]1CN(C(=O)C2COC2)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 7, 1, 7, 1, 1, 1, 1, 19, 19, 19, 19, 28, 28, 28, 32, 32, 32, 32, 32, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 19, 19, 28, 32] 32 rigid atoms, others: [32, 5, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35, 36]) total number of confs: 74 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074883 none C[C@@H]1CN(C(=O)C2COC2)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 19, 19, 19, 1, 1, 1, 1, 5, 5, 5, 15, 15, 15, 15, 15, 2, 2, 2, 1, 1, 19, 19, 19, 19, 19, 1, 1, 5, 15] 32 rigid atoms, others: [0, 1, 2, 3, 4, 5, 33, 11, 12, 34, 14, 13, 26, 27] set([6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 35, 36]) total number of confs: 81 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.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: REAL250005074883 none C[C@@H]1CN(C(=O)C2COC2)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 15, 15, 24, 24, 32, 32, 32, 15, 8, 15, 8, 1, 8, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 32, 32, 32, 32, 32, 15, 15, 8, 1] 32 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: 103 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074883 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074883 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074883/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074883 Building REAL250005074884 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074884' /scratch/stefan/7916156/working/building/REAL250005074884 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074884 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074884/0 /scratch/stefan/7916156/working/building/REAL250005074884 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 1006) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/1006 `/scratch/stefan/7916156/working/3D/1006' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C=CCO)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005074884.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074884/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074884 none C[C@@H]1CN(C(=O)C=CCO)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 5, 12, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 222 conformations in input total number of sets (complete confs): 222 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 23, 23, 23, 23, 45, 45, 71, 71, 74, 23, 8, 23, 8, 1, 8, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 71, 71, 74, 74, 222, 23, 23, 9, 1] 222 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: 449 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074884 none C[C@@H]1CN(C(=O)C=CCO)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 5, 12, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 222 conformations in input total number of sets (complete confs): 222 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 28, 28, 61, 1, 1, 1, 1, 5, 5, 5, 23, 23, 23, 23, 23, 2, 2, 2, 1, 1, 28, 28, 61, 61, 183, 1, 1, 5, 23] 222 rigid atoms, others: [0, 1, 2, 3, 4, 5, 33, 11, 12, 34, 14, 13, 26, 27] set([6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 35, 36]) total number of confs: 443 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074884 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074884 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074884/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074884 Building REAL250005074885 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074885' /scratch/stefan/7916156/working/building/REAL250005074885 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074885 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074885/0 /scratch/stefan/7916156/working/building/REAL250005074885 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 1007) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/1007 `/scratch/stefan/7916156/working/3D/1007' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC=CC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074885.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074885.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074885/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074885 none CCC=CC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [80, 69, 69, 49, 22, 49, 22, 22, 22, 22, 22, 10, 22, 10, 1, 10, 1, 1, 1, 1, 1, 1, 22, 80, 80, 80, 80, 80, 69, 69, 22, 22, 22, 22, 22, 11, 1, 22, 22] 80 rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 273 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074885 none CCC=CC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [51, 30, 30, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 22, 22, 22, 22, 22, 1, 51, 51, 51, 51, 51, 29, 30, 1, 1, 2, 2, 2, 5, 22, 1, 1] 80 rigid atoms, others: [4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 22, 38, 30, 31] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 231 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074885 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074885 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074885/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074885 Building REAL250005074886 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074886' /scratch/stefan/7916156/working/building/REAL250005074886 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074886 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074886/0 /scratch/stefan/7916156/working/building/REAL250005074886 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 1008) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/1008 `/scratch/stefan/7916156/working/3D/1008' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074886.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074886/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074886 none C#CCCC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [75, 75, 71, 33, 12, 33, 12, 12, 12, 12, 12, 6, 12, 6, 1, 6, 1, 1, 1, 1, 1, 1, 12, 75, 75, 75, 71, 71, 12, 12, 12, 12, 12, 6, 1, 12, 12] 75 rigid atoms, others: [34, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36]) total number of confs: 282 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074886 none C#CCCC(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [53, 52, 34, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 12, 12, 12, 12, 1, 53, 52, 52, 34, 34, 1, 1, 2, 2, 2, 5, 12, 1, 1] 75 rigid atoms, others: [35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 22, 36, 28, 29] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34]) total number of confs: 246 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074886 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074886 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074886/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074886 Building REAL250005074887 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074887' /scratch/stefan/7916156/working/building/REAL250005074887 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074887 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074887/0 /scratch/stefan/7916156/working/building/REAL250005074887 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 1009) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/1009 `/scratch/stefan/7916156/working/3D/1009' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(O)C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074887.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074887/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074887 none C=CC(O)C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 171 conformations in input total number of sets (complete confs): 171 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 37, 57, 15, 37, 15, 15, 15, 15, 15, 7, 15, 7, 1, 7, 1, 1, 1, 1, 1, 1, 15, 57, 57, 57, 57, 171, 15, 15, 15, 15, 15, 7, 1, 15, 15] 171 rigid atoms, others: [34, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36]) total number of confs: 366 number of broken/clashed sets: 19 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074887 none C=CC(O)C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 171 conformations in input total number of sets (complete confs): 171 using faster count positions algorithm for large data unique positions, atoms: [40, 26, 7, 26, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 15, 15, 15, 1, 40, 40, 40, 26, 78, 1, 1, 2, 2, 2, 5, 15, 1, 1] 171 rigid atoms, others: [35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 22, 36, 28, 29] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34]) total number of confs: 251 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074887 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074887 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074887/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074887 Building REAL250005074888 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074888' /scratch/stefan/7916156/working/building/REAL250005074888 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074888 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074888/0 /scratch/stefan/7916156/working/building/REAL250005074888 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 1010) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/1010 `/scratch/stefan/7916156/working/3D/1010' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074888.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074888/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074888 none CC(O)C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [20, 18, 20, 10, 18, 10, 10, 10, 10, 10, 5, 10, 5, 1, 5, 1, 1, 1, 1, 1, 1, 10, 20, 20, 20, 20, 60, 10, 10, 10, 10, 10, 6, 1, 10, 10] 60 rigid atoms, others: [33, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35]) total number of confs: 123 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074888 none CC(O)C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [16, 7, 16, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 10, 10, 10, 10, 1, 16, 16, 16, 16, 48, 1, 1, 2, 2, 2, 5, 10, 1, 1] 60 rigid atoms, others: [34, 3, 5, 6, 7, 8, 9, 10, 11, 12, 35, 21, 27, 28] set([0, 1, 2, 4, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 127 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074888 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074888 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074888/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074888 Building REAL250005074889 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074889' /scratch/stefan/7916156/working/building/REAL250005074889 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074889 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074889/0 /scratch/stefan/7916156/working/building/REAL250005074889 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 1011) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/1011 `/scratch/stefan/7916156/working/3D/1011' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074889.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074889/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074889 none CC(=O)C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [24, 17, 24, 11, 17, 11, 11, 11, 11, 11, 5, 11, 5, 1, 5, 1, 1, 1, 1, 1, 1, 11, 24, 24, 24, 11, 11, 11, 11, 11, 6, 1, 11, 11] 24 rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33]) total number of confs: 77 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074889 none CC(=O)C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 16, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 11, 11, 11, 11, 11, 1, 15, 15, 15, 1, 1, 2, 2, 2, 5, 11, 1, 1] 24 rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 10, 11, 12, 21, 25, 26] set([0, 1, 2, 4, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 27, 28, 29, 30, 31]) total number of confs: 64 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074889 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074889 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074889/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074889 Building REAL250005074890 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074890' /scratch/stefan/7916156/working/building/REAL250005074890 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074890 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074890/0 /scratch/stefan/7916156/working/building/REAL250005074890 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 1012) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/1012 `/scratch/stefan/7916156/working/3D/1012' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)C2(F)CC2)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1) `REAL250005074890.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074890/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074890 none C[C@@H]1CN(C(=O)C2(F)CC2)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 9, 1, 9, 1, 1, 1, 1, 23, 23, 23, 23, 30, 30, 30, 31, 31, 31, 31, 31, 23, 23, 23, 23, 23, 1, 1, 1, 1, 23, 23, 30, 31] 31 rigid atoms, others: [5, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35]) total number of confs: 67 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074890 none C[C@@H]1CN(C(=O)C2(F)CC2)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 23, 23, 23, 1, 1, 1, 1, 5, 5, 5, 11, 11, 11, 11, 11, 2, 2, 2, 1, 1, 23, 23, 23, 23, 1, 1, 5, 11] 31 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 11, 12, 13, 14, 33, 26, 27] set([6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 34, 35]) total number of confs: 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.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: REAL250005074890 none C[C@@H]1CN(C(=O)C2(F)CC2)C[C@@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 25, 25, 31, 31, 31, 11, 5, 11, 5, 1, 5, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 31, 31, 31, 31, 11, 11, 5, 1] 31 rigid atoms, others: [35, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 91 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074890 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074890 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074890/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074890 Building REAL250005074891 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074891' /scratch/stefan/7916156/working/building/REAL250005074891 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074891 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074891/0 /scratch/stefan/7916156/working/building/REAL250005074891 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 1013) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/1013 `/scratch/stefan/7916156/working/3D/1013' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=C(F)C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074891.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074891/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074891 none CC=C(F)C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 25, 30, 11, 25, 11, 11, 11, 11, 11, 6, 11, 6, 1, 6, 1, 1, 1, 1, 1, 1, 11, 30, 30, 30, 30, 11, 11, 11, 11, 11, 6, 1, 11, 11] 30 rigid atoms, others: [33, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35]) total number of confs: 91 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074891 none CC=C(F)C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [21, 20, 6, 21, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 11, 11, 11, 11, 11, 1, 20, 21, 21, 20, 1, 1, 2, 2, 2, 5, 11, 1, 1] 30 rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 22, 27, 28] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 81 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074891 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074891 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074891/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074891 Building REAL250005074892 mkdir: created directory `/scratch/stefan/7916156/working/building/REAL250005074892' /scratch/stefan/7916156/working/building/REAL250005074892 /scratch/stefan/7916156/working /scratch/stefan/7916156 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005074892 mkdir: created directory `0' /scratch/stefan/7916156/working/building/REAL250005074892/0 /scratch/stefan/7916156/working/building/REAL250005074892 /scratch/stefan/7916156/working /scratch/stefan/7916156 Protomer 0 (index: 1014) Found valid previously generated 3D confromation in /scratch/stefan/7916156/working/3D/1014 `/scratch/stefan/7916156/working/3D/1014' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CO)C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005074892.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005074892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916156/working/building/REAL250005074892/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074892 none CC(CO)C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [27, 21, 27, 27, 8, 21, 8, 8, 8, 8, 8, 4, 8, 4, 1, 4, 1, 1, 1, 1, 1, 1, 8, 27, 27, 27, 27, 27, 27, 81, 8, 8, 8, 8, 8, 4, 1, 8, 8] 81 rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 174 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005074892 none CC(CO)C(=O)N1C[C@@H](C)[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 13, 24, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 8, 8, 8, 1, 13, 13, 13, 13, 24, 24, 72, 1, 1, 2, 2, 2, 5, 8, 1, 1] 81 rigid atoms, others: [4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 22, 38, 30, 31] set([0, 1, 2, 3, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 192 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916156/working/building/REAL250005074892 /scratch/stefan/7916156/working /scratch/stefan/7916156 Finished preparing REAL250005074892 Recording results /scratch/stefan/7916156/working /scratch/stefan/7916156 Appending to /scratch/stefan/7916156/finished/xaaaabk.* 0: /scratch/stefan/7916156/working/building/REAL250005074892/0.* Removing working files in /scratch/stefan/7916156/working/building/REAL250005074892 /scratch/stefan/7916156 Compressing combined databse files /scratch/stefan/7916156/finished/xaaaabk.db2.gz /scratch/stefan/7916156/finished/xaaaabk.solv.gz ======================================================= WARNING: STORE_PROTOMERS not executable or a directory! All results left in place (/scratch/stefan/7916156/finished) ======================================================= Finalizing... removed `/scratch/stefan/7916156/working/3D/1015' removed directory: `/scratch/stefan/7916156/working/3D' `/scratch/stefan/7916156/working/protonate' -> `/scratch/stefan/7916156/archive' `/scratch/stefan/7916156/working/input-smiles.ism' -> `/scratch/stefan/7916156/archive/input-smiles.ism' rmdir: removing directory, `/scratch/stefan/7916156/working/building' rmdir: removing directory, `/scratch/stefan/7916156/working' ls: No match. ls: No match.